This happens if a XRC files does have a wrong or no version number. I'm afraid you've to disable the plugins step by step to see what causes the issue.
disable and enable it can't find the wrong xrc files. Instead, I set a breakpoint in bool Manager::LoadResource(const wxString& file), and check each zip file manually(the zip file name can be seen as the function argument) to see whether they have wrong xrc files.
Here are 5 wrong files I just caught:
manager_resources.zip
edit_keywords.xrc
project_deps.xrc
project_options.xrc
virtualbuildtargetsdlg.xrc
codecompletion.zip
goto_function_dlg.xrc
FYI: Just set a breakpoint in the file:
"wxXmlResource::DoLoadFile (this=0x58b2b88, filename=...) at D:\wx3\src\xrc\xmlres.cpp:772"
can catch all such warnings.
if (m_version != version)
{
wxLogWarning("Resource files must have same version number.");
}