When a workspace is loaded and DebuggerManager::OnProjectActivated is called, FindTargetsDebugger is bypassed because of the statement
void DebuggerManager::FindTargetsDebugger()
{
    if (Manager::Get()->GetProjectManager()->IsLoadingOrClosing())
        return;
Thus, the correct debugger is not setup for the project, since IsLoadingOrClosing() is *always* true during OnProjectActivated for workspace loading. (At some point, CB code was changed to leave m_IsLoadingProject at true during OnProjectActivated to avoid a CC problem).
Adding
+    Manager::Get()->RegisterEventSink(cbEVT_PROJECT_OPEN, new Event(this, &DebuggerManager::OnProjectActivated));
solves the problem, since at that call, IsLoadingOrClosing() is false.
Index: src/sdk/debuggermanager.cpp
===================================================================
--- src/sdk/debuggermanager.cpp	(revision 8647)
+++ src/sdk/debuggermanager.cpp	(working copy)
@@ -674,6 +674,7 @@
 {
     typedef cbEventFunctor<DebuggerManager, CodeBlocksEvent> Event;
     Manager::Get()->RegisterEventSink(cbEVT_PROJECT_ACTIVATE, new Event(this, &DebuggerManager::OnProjectActivated));
+    Manager::Get()->RegisterEventSink(cbEVT_PROJECT_OPEN, new Event(this, &DebuggerManager::OnProjectActivated));
     Manager::Get()->RegisterEventSink(cbEVT_BUILDTARGET_SELECTED, new Event(this, &DebuggerManager::OnTargetSelected));
     Manager::Get()->RegisterEventSink(cbEVT_SETTINGS_CHANGED, new Event(this, &DebuggerManager::OnSettingsChanged));
     Manager::Get()->RegisterEventSink(cbEVT_PLUGIN_LOADING_COMPLETE,
svn build  rev 8647 (2012-12-09 23:28:42)   gcc 4.3.1 Windows/unicode - 32 bit