Itunes does not sync iphone

Hello
today, I have a new problem:
My iphone (4) does not synch with itunes (10.6 (7), although it is recognized and displayed. when I activate the "sync"-command, itunes says "waiting for iphone to synchronize until it times out.
After resetting the phone, which worked, I used the last backup (which worked), but all my 3rd-party apps are now gone.
Disabling all media-sync did not work.
It is to say that I have 2 apple-accounts, an old one, with which I made all media- and app-purchases, and a newer me.com account, which I use to sync my data (mail, address-book, ical) through icloud.
I suspect this dual apple-ID-thing to be the problem, is that so?
As far as I know, there is no possibility to update an app from the old registration-ID to the newer one? ( I would prefer to stick with me.com, although most of the apps run under the old ID)
Thanks for help!

All purchased apps, books, music, movies, etc are forever tied to the Apple ID used. You can use the same Apple ID for syncing with the iCloud. The me.com account is a free iCloud e-mail.

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