Did you try to build C::B from a fresh svn-checkout ?
And did you remove all occurrences of older C::B versions on your system ?
I am using Gnome version 2.22.3 as supplied by Ubuntu. I don't know anything about "composite effects" -- what they are or whether they are enabled. Can you tell me what to look for?
Something like transparent windows while moving and/or transparent window decorations, but that should not harm C::B (at least not in this way).
I don't have ubuntu 8.04 and no (working) nvidia-card to test this behaviour.
I have several linux and windows systems (mostly on kvm-virtual machines) some of them with 32- and 64-bit (kubuntu 9.04, ubuntu 9.10, centos 5.4, openSUSE 11.2, w2k, winxp, vista, win7-64-bit-release-candidat), but no such issues on any of them.
So my idea is to remove everything below <prefix>/lib/codeblocks, <prefix>/share/codeblocks before installing a fresh build
I suggest to run make uninstall first, and then look if anything is left from former installs (the directory layout has changed a little bit, to move the binary parts of the plugins from the share-folder into the lib-folder, so there might be some files left).
Maybe that helps, I have no other idea at the moment.