Restoring backup doesn't work! Iphone 3GS, Itunes 9

I live in Holland, but I presently am in Japan. In Japan I made a backup of my Iphone. Afterward I tried to install some apps I downloaded through Itunes (while still being in Japan). When I tried to put the apps on my Phone I received the message stating it would delete apps that weren't on the computer yet. So I authorized this computer (using my login data) and started syncing, even though the message still appeared. As a result I now have only a few apps left. Most of them have been removed from my Iphone and strangely, none of the apps I downloaded here (in Japan) were put on the Iphone!?!?!
So I did a restore. Yet, strangely, I don't get my original apps back.
I even restored the original Backup folder from a couple of days ago, so everything should be there.
Does anybody have an idea what the problem is?

Iphone will sync apps with only one computer at a time. If you sync to another computer, then it will erase the current content from the iphone first, then replace with content from the new computer.
The itunes backup that iphone does while syncing doe not include apps:
http://support.apple.com/kb/HT1766

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Thanks a lot for your advice.
Deleting the correupted back up means to delete the information of one month since the last back up I made is one month ago.....right?
This back up I made right before I restored my iphone. During the restore however my OS was upgraded to 5.1.1. and reading the comments on the internet it seems I am not the only one whom experience this problem.
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Message was edited by: loop_digga

Ok, I tried everything, last thing I did was downgrading and reinstaling iTunes, also without any good results, so unfortunately I had to do Restore. To be completly shure that previous backup was reason of errors, I set device as new, and now it is ok

Restoring backup doesn't work! Iphone 3GS, Itunes 9

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