I did some basic testing on Windows using Ogre 1.4.7 and v0-6 branch code (basically what will become 0.6.1, though no relevant changes have been made from 0.6.0 that would affect any tests).
I integrated the new CEGUI into Ogre and ran the Ogre sample apps that use cegui, with the Ogre supplied CEGUI datafiles - no issues there.
I then integrated Ogre and the updated Ogre CEGUI renderer into the CEGUI samples and ran those, using the CEGUI supplied datafiles - no issues there.
Is it just like your 'main app' that you get the issue with, if you have such a thing, or does a minimal example also demonstrate the issues?
Do you use a different scene manager or anything of that nature?
Do you use a stock Ogre, or are there mods?
Since you upgraded CEGUI in what might be considered an 'unusual' way (using diffs), does this mean you had existing mods to CEGUI? If so what were/are they? In either case, how does the CEGUI you're using differ now from the 0.6.0 release code?
There's obviously something going on, while I think it's definitely not "us", there is an outside possibility of some strangeness or possible missing render setting in the CEGUI renderer module for Ogre (hence, some of the questions). Failing that it must be something modified or app/client side (hence the rest of the questions!).
If you're convinced it's not something local to your own app (and I guess you would be if it only broke due to the upgrade), what would be most useful right now is a minimal example that demonstrates the issue
CE.