Thanks for your quick answer. I can confirm that behaviour... i had the same "problem" and did the restore twice. The third time i just hit "set up as new phone" and it did keep all the history stuff.
By the way, i did backup all the data in /private/var/mobile/Library/ via sftp just in case that setup as new phone went wrong. But i didn't... everything is there.
At the moment it's synching the media files just fine... :)
What I'd like to know is why some people are experiencing this problem, while others are not. Has anyone tried rebuilding a custom firmware file with PwnageTool from an official source and restoring (non-DFU the second time) to see if the problem recurs?
I was on Pwnage2.0.1 with Firmware 2.0 and it was working perfect on iTunes 7.6 (???) or the one before current (7.7).... then I upgraded to the latest iTunes (7.7), and that happened, yesterday, then Pwnage2.0.2 came out, Pwn'd the iPhone and I'm still having this problem.
Same exact situation happened to my roomate, with an iPhone 3G.
It's got to be related to iTunes 7.7
PwnageTool_2.0.2.tbz was the file I downloaded, from the mirror in the iphone dev team's blog directly...
I just downgraded itunes version and everything is back to normal.
I just encountered the same problem.
Pwned 2.0.1, restored the custom ipsw with itunes, restored my iphone backup. the progress bar stopped at some time and after about 5 minutes my iPhone booted, iTunes detected it again and offered to restore the data again.
I created a new one which I'm synching right now.
I used a sparkle-updated Pwnagetool, iTunes 7.7.1.
I hope there are no other problems involved now...
I downloaded a new version of PwnageTool, checked the SHA, rebuilt a custom firmware package, and redid a DFU restore. Same problem! At least this time I knew to choose "new iPhone" for the second restore.
I think that this is a problem with PwnageTool, as I couldn't find any complaints on the Apple discussion forums.