ITunes 9.2.1 (4) tries to update a "ghost" application, show inconsistencie

Question

Hi to all,
I recently needed to reinstall the computer from a Time Machine backup, and encountered four issues:
1- iTunes seems to be unable to find my library, and my library doesn't appear; no music track, no podcast, no nothing. However, strange it still shows the previous iPod Touch saves I made.
2- iTunes is unable to remember my Apple Store password. There's no tickbox to remember it??
3- iTunes keeps on trying to update a non-existent application. I verified, and this application has completely disappeared from the computer, but iTunes still tries to update it, and it always ends up with error 8012. I looked for this error on the Web, but seems to be unknown under Mac
4- Maybe linked to the second issue, iTunes is the only application that asks, each time it's launched, to be allowed incoming connections, although "allow" incoming connections is already set in the firewall.
I don't know exactly where to start to solve these behavioral inconsistencies.

Answer 1

A year and a half later, manually upgraded all the way to iTunes 10.5.3, since Software update is unable to update iTunes properly. In the meantime, both of my iPods (Touch and Shuffle) were stolen.
Issues 1 and 4 have disappeared, but 2 and 3 remain.
Still no answer. I can't believe nobody had this issue.