Time machine great but programs crash

Hello all,
Just wanted to say how relieved I was to have upgraded and been using Time Machine. Hard drive crashed, got new one, recovered from TM and everything came back exactly as it was.
However.
I can't say for sure this has anything to do with TM, but every other program I had installed previously was up and running exactly as it was before except for iWeb, iMovie HD, iDVD and Photo Booth.
None of those programs will open now. Coincidence? I don't know.
When I got the machine back, I got all software updates and repaired permissions. In Photo Booth, the first program I noticed the problem in, I removed the preference file and restarted and still nothing. And before someone tells me to zap the PRAM, can you tell me if i will lose preferences in all my programs?
What do I do, aside from putting my machine back in for service and losing more work due to lost time?
Thanks for help,
Mj

Time machine working perfectly well with my 24" iMac (with an external USB HD) and used to work fine with my Power G5 (internal extral HD) - but after I did the Erase and install of the OS on my Power G5 (upgraded to 10.5.1) - it is just crashing my computer twice, still finding a way to fix it

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