Very few changes actually were necessary to get everything to compile and work together. Code::Blocks is a very stable program IMHO.
First thing to take into account: my binaries are not compatible with the Code::Blocks Team binaries: they use wxWidgets 2.8.10, and I use wxWidgets 2.8.11. There are a few notable differences that were noticed while testing - part of the reason why 2.8.11 wasn't adopted by the official developers yet.
I only undefined WX_PRECOMP in order to compile cbDiff, and changed the placing of the option in the File menu. Not a big deal, though maybe I should warn the author about this.
I also made a minor change that has zero impact on SpellChecker functionality: I changed the default dictionary to en_US (to match the bundled dictionaries). Hardly worth a patch IMHO.
FileManager, as it so happens, was not changed at all, so I'm not certain of how I may have caused the runtime crash.
EDIT: I tried it on my setup and could cause a crash, but I think it's FileManager related. Which path (which kind of files, and with what permissions) were you trying to navigate to?
If you could take the time to build the svn trunk and FileManager yourself, test it in a setup that is closer to what is used for the nightly builds, and confirm the crash, then we should contact the FileManager author. There are helpful links in the installer disclaimer.