So I am leaning toward this being an issue caused by auto-layout and the chance of creating a workaround is small.
But it is very interesting that during the last few days, I also seem to have seen this bug a lot, where before, it was a rare occurrence.
It would be interesting to know if anyone is seeing it on 10.10.
I'm running TM 2.0-beta.6 on Yosemite 10.10.1 (14B25) and I don't encounter any issues working either with the "Find in Project" or the "Filter Through Command" windows. The UI is fully responsive.
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