Yep, thats the problem, to stop the headache inmmediatley just replaced the member with this:
Index: src/plugins/contrib/AutoVersioning/AutoVersioning.cpp
===================================================================
--- src/plugins/contrib/AutoVersioning/AutoVersioning.cpp	(revision 5005)
+++ src/plugins/contrib/AutoVersioning/AutoVersioning.cpp	(working copy)
@@ -65,7 +65,6 @@
     ProjectLoaderHooks::HookFunctorBase* AutoVerHook =
       new ProjectLoaderHooks::HookFunctor<AutoVersioning>(this, &AutoVersioning::OnProjectLoadingHook);
     m_AutoVerHookId = ProjectLoaderHooks::RegisterHook(AutoVerHook);
-    m_IsCurrentProjectVersioned = false;
     m_Modified = false;
     m_Project = 0;
 } // end of constructor
@@ -128,11 +127,11 @@
 		// TODO (KILLERBOT) : should we have default values, in case something would be missing ?
 		// OPTI : we could choose not to write out default values in the xml --> smaller cbp
 		avConfig Config;
-		m_IsCurrentProjectVersioned = false; // default not active unless we find xml for it
+		m_IsVersioned[project] = false; // default not active unless we find xml for it
 		const TiXmlElement* Node = elem->FirstChildElement("AutoVersioning");
 		if (Node)
 		{
-			m_IsCurrentProjectVersioned = true;
+			m_IsVersioned[project] = true;
 			TiXmlHandle Handle(const_cast<TiXmlElement*>(Node));
 			if(const TiXmlElement* pElem = Handle.FirstChildElement("Scheme").ToElement())
 			{
@@ -215,7 +214,6 @@
         }
 		m_ProjectMap[project] = Config;
 		m_ProjectMapVersionState[project] = VersionState;
-		m_Project = project;
 	}
 	else
 	{
@@ -226,7 +224,7 @@
 		// if plugins that use that element are not loaded atm).
 		// so, instead of blindly inserting the element, we must first check it's
 		// not already there (and if it is, clear its contents)
-		if(m_IsCurrentProjectVersioned)
+		if(m_IsVersioned[project])
 		{
 			TiXmlElement* node = elem->FirstChildElement("AutoVersioning");
 			if (!node)
@@ -281,7 +279,8 @@
 	if (IsAttached())
 	{
 		m_ProjectMap.erase(event.GetProject());
-		m_ProjectMapVersionState.erase(event.GetProject());
+		m_ProjectMapVersionState.erase(event.GetProject());
+        m_IsVersioned.erase(event.GetProject());
 		if(m_Project == event.GetProject())
 		{   // should always be the case (??? we hope ??)
 		    m_Project = 0;
@@ -294,7 +293,7 @@
 // be activated and each has the compilerstarted/Finished ?????
 void AutoVersioning::OnCompilerStarted(CodeBlocksEvent& event)
 {
-    if (m_Project && IsAttached() && m_IsCurrentProjectVersioned)
+    if (m_Project && IsAttached() && m_IsVersioned[event.GetProject()])
     {
 		if (m_Modified)
 		{
@@ -317,7 +316,7 @@
 
 void AutoVersioning::OnCompilerFinished(CodeBlocksEvent& event)
 {
-    if (m_Project && IsAttached() && m_IsCurrentProjectVersioned)
+    if (m_Project && IsAttached() && m_IsVersioned[event.GetProject()])
 	{
 		++(GetVersionState().Values.BuildCount);
 	}
@@ -325,7 +324,7 @@
 
 void AutoVersioning::OnTimerVerify(wxTimerEvent& event)
 {
-    if (m_Project && IsAttached() && m_IsCurrentProjectVersioned)
+    if (m_Project && IsAttached() && m_IsVersioned[m_Project])
     {
 		if (!m_Modified)
 		{
@@ -348,7 +347,7 @@
     {
         if (m_Project)
         {
-            if (m_IsCurrentProjectVersioned)
+            if (m_IsVersioned[m_Project])
             {
                 SetVersionAndSettings(*m_Project, true);
                 UpdateVersionHeader();
@@ -357,8 +356,20 @@
             {
                 if (wxMessageBox(_("Configure the project \"") + m_Project->GetTitle() + _("\" for Autoversioning?"),_("Autoversioning"),wxYES_NO) == wxYES)
                 {
+                    if(wxFileExists(m_Project->GetBasePath() + _T("version.h")))
+                    {
+                        wxMessageBox(
+                         _T("The header version.h already exist on your projects path. "
+                            "The content will be overwritten by the the version info generated code."
+                            "\n\nYou can change the default version.h file on the \"Settings\" Tab."
+                           ),
+                         _T("Warning"),
+                         wxICON_EXCLAMATION  | wxOK
+                        );
+                    }
+
 					// we activated
-					m_IsCurrentProjectVersioned = true;
+					m_IsVersioned[m_Project] = true;
 					// just becasue we activated the project becomes modified
 					m_Project->SetModified();
 
@@ -382,7 +393,7 @@
 
 void AutoVersioning::OnMenuCommitChanges(wxCommandEvent&)
 {
-    if (m_Project && IsAttached() && m_IsCurrentProjectVersioned)
+    if (m_Project && IsAttached() && m_IsVersioned[m_Project])
     {
         if(m_Modified)
         {
@@ -406,7 +417,7 @@
             {
                 event.Enable(true);
             }
-            else if (m_IsCurrentProjectVersioned)
+            else if (m_IsVersioned[m_Project])
             {
                 if (m_Modified)
                 {
@@ -528,9 +539,15 @@
 {
     m_timerStatus->Stop();
 
+    //Declares the header guard to be used based on the filename
+    wxFileName filename(cbC2U(GetConfig().Settings.HeaderPath.c_str()));
+    wxString headerGuard = filename.GetName() + _T("_") + filename.GetExt();
+    headerGuard.Replace(_T(" "), _T("_"), true);
+    headerGuard.UpperCase();
+
     wxString headerOutput = _T("");
-    headerOutput << _T("#ifndef VERSION_H") << _T("\n");
-    headerOutput << _T("#define VERSION_H") << _T("\n");
+    headerOutput << _T("#ifndef ") << headerGuard << _T("\n");
+    headerOutput << _T("#define ") << headerGuard  << _T("\n");
     headerOutput << _T("\n");
 
     if(cbC2U(GetConfig().Settings.Language.c_str()) == _T("C++"))
@@ -610,9 +627,9 @@
         headerOutput << _T("}") << _T("\n");
     }
 
-    headerOutput << _T("#endif //VERSION_h\n");
+    headerOutput << _T("#endif //") << headerGuard << _T("\n");
 
-    m_versionHeaderPath = FileNormalize(cbC2U(GetConfig().Settings.HeaderPath.c_str()),m_Project->GetBasePath());;
+    m_versionHeaderPath = FileNormalize(cbC2U(GetConfig().Settings.HeaderPath.c_str()),m_Project->GetBasePath());
     wxFile versionHeaderFile(m_versionHeaderPath, wxFile::write);
     versionHeaderFile.Write(headerOutput);
     versionHeaderFile.Close();
@@ -622,7 +639,7 @@
 
 void AutoVersioning::CommitChanges()
 {
-    if (m_Project && IsAttached() && m_IsCurrentProjectVersioned)
+    if (m_Project && IsAttached() && m_IsVersioned[m_Project])
     {
         if (m_Modified)
         {
Index: src/plugins/contrib/AutoVersioning/AutoVersioning.h
===================================================================
--- src/plugins/contrib/AutoVersioning/AutoVersioning.h	(revision 5005)
+++ src/plugins/contrib/AutoVersioning/AutoVersioning.h	(working copy)
@@ -56,10 +56,10 @@
     wxTimer* m_timerStatus;
     int m_AutoVerHookId; //!< project loader hook ID
     std::map<cbProject*, avConfig> m_ProjectMap;
-    std::map<cbProject*, avVersionState> m_ProjectMapVersionState;
+    std::map<cbProject*, avVersionState> m_ProjectMapVersionState;
+    std::map<cbProject*, bool> m_IsVersioned;
     cbProject* m_Project; // keeps track of the last 'activated' project
     bool m_Modified; // have some settings been modified
-    bool m_IsCurrentProjectVersioned;
     /// fires when a project is being loaded / saved
     void OnProjectLoadingHook(cbProject* project, TiXmlElement* elem, bool loading);
 
Index: src/plugins/contrib/AutoVersioning/manifest.xml
===================================================================
--- src/plugins/contrib/AutoVersioning/manifest.xml	(revision 5005)
+++ src/plugins/contrib/AutoVersioning/manifest.xml	(working copy)
@@ -3,7 +3,7 @@
     <SdkVersion major="1" minor="10" release="0" />
     <Plugin name="AutoVersioning">
         <Value title="AutoVersioning" />
-        <Value version="1.1" />
+        <Value version="1.2" />
         <Value description="Auto increments the version and build number of your application every time a change has been made and stores it in version.h with easy to use variable declarations. Also have a feature for committing changes a la SVN style, a version scheme editor and a change log generator.
 
 Example:
@@ -40,7 +40,7 @@
 	  static const char SVN_REVISION[]
 	  static const char SVN_DATE[]
 " />
-        <Value author="JGM" />
+        <Value author="Jefferson Gonzalez" />
         <Value authorEmail="jgmdev@gmail.com" />
         <Value authorWebsite="" />
         <Value thanksTo="Killerbot - Code Optimizations, conversion from version.ini to project file and many more...