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I've never had an issue like this with LPP. I've been using the paid version since a month after I got the phone, too.
Are you sure it was Launcher Pro? Maybe it was something interacting with LPP and was actually masking the problem? Not meaning to be insulting or anything by asking this, but is it a fully legit copy?
I started getting random reboots when I fsbfed back to stock froyo, and found the perpetrator to be launcher pro plus. Just wondering if anybody else is having this issue, or if its something in the flashing back I did.