Digging into things a bit more, the issue doesn't seem to be with GL interop, but rather with the clAmdFFT library from the APP Math Libraries package. It seems to have somehow lost a bunch of precision when used with Catalyst 11.6.
Anyone else experiencing sudden problems with clAmdFFT with Catalyst 11.6?
Interestingly, updating to the Catalyst 11.6b hotfix cleared this up, if anyone else stumbled across this having similar problems. Guess it was in fact a driver issue and I'm not going crazy after all :)
Hope this fix gets deployed more widely soon; I can't release my app to consumers while the latest publicly available drivers have this issue.