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There are no particular Oracle parameter value changesrequired for Windchill on11gR2 versus 10g. Since you didn't upgrade Windchill, there isn't any possibility that any custom indexes were dropped, although you should be checking for invalid packages and indexes that might need updating. Make sure your nightly stats job is running successfully. Check ADDM & AWR reports for any weirdness. I'massuming the datafile dispersion and other hardware remained the same during the upgrade, and you've verified that you have all required o/s patches for 11gR2.
Other than those general Oracle things, treat this a new performanceissue. I'd suggest generating a Oracle Tuning Report (aka gather_info) after one of these checkins is complete and opening a TS call for analysis.
Tim Atwood
PTC Enterprise Deployment Center
After the database upgrade, all the tables/index has been analysed? Please check the fragmentation also. May be a database reorg is needed.