I just installed and imported our 60K defects and features from TeamTrack into OnTime 2009 and am seeing horrible performance as well.
The performance degredation is everywhere, but to give a specific example:
If I have a project with 400 defects in it and I text in the "Search for" field and filter it to a particular field (the Notes field for instance), it takes around 1 minute to display the resulting 20 items. It is as if it is crawling all 60K items to check the search against rather than just the 400 in the selected project...
We are running on SQL Server on a Dual Quad Core (2 Quad Core Processors) box with 4G of RAM...