Will old iMac problems transfer to the new one?

My present Intel iMac is having firewire issues and past its warranty, so I'm going for a new iMac. In an effort to try and salvage the old one I wiped everything clean, reinstalled the the OS and restored from a Time Machine backup. Now I'm having problems that weren't there before, like not being able to open Mail, iTunes, or Safari.
The new iMac arrives on Monday, but I'm worried that whatever is wrong with the old computer will transfer into the new one. Any ideas on how to avoid this?

That's a good thought on the 3rd party apps. I'm taking inventory of all my disks and downloadable Apps now, and removing them so I can individually reinstall them on the new machine.
I checked out the permissions and everything seems to be OK. But still no luck on the those three apps. Mail opens, but crashes as soon as I try to read a message. And iTunes and Safari can't stay open at all. Interestingly enough, I'm trying other Mac apps like iCal, Garage Band and iPhoto and they're all still good.

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