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*UPDATE*
Another possible solution to this problem is to put the iPhone in Safe Mode (using SBSettings) before you Sync with iTunes. I didn't try to sync but iTunes displayed everything correctly when my phone was in safe mode.
 
I have a similar problem. I have a 3G that was running 4.0 until yesterday, when I jailbroke it using a popular online tool (that I'm not sure I can name :p).

I had an App Store-bought app on my phone beforehand that records audio (iPodcaStudio), and due to a bug it can't delete clips, so I deleted it off the phone and attempted to resync the app back after backing up the clips. I can't, however, sync this app back to the phone.

When I plug my phone into my computer, the app sync tab has the icons for everything that is currently on the phone but a blank white App Store icon for everything that isn't. Even though the iPodcaStudio app is checked, it won't transfer to my phone.

I had FiveIconDock installed but removed it after reading above it may be the problem. I have also tried to sync in Safe Mode with no success. I'm about to uninstall and reinstall iTunes but if anyone has any help it would be appreciated.

I'm running Windows 7 Ultimate and iTunes 9.2.1.5 if it helps.

EDIT: Okay, this may not be an issue with the jailbreak itself. I transferred my iTunes library between computers a while ago and may not hav transferred the apps - it looks like all the ones with the white squares are ones I downloaded before the transfer. To test, I'll delete one I've added post-transfer and see if it syncs.

EDIT: Yeah, this isn't a JB issue. All my apps were in the wrong folder. Sorted now.
 
You have to disable or uninstall any app you have that changes the icon or dock layout. Apps like Infinidock, FivecolumnSB, FiveIcondock, etc. I played around with it for a while and discovered Infinidock was causing the problem for me. I had to completely uninstall it thru Cydia in order for iTunes to read my phone correctly. If you're using FivecolumnSB you can simply disable it thru it's options. I assume that any app that makes changes to your icon and/or dock layout causes this problem. Just uninstall or disable all of these types of apps that you have, restart your springboard, sync your phone, then re-enable and re-install the apps that cause the problem. I hope this helps. It worked for me.

Yes. Thank you! This fixed it for me. :)

I had the Five Icon Dock installed via Cydia and as soon as I removed it (via Cydia) my folders showed up fine when trying to sync. No more disappearing or losing folders on my iPhone 3GS (5.0.1) when syncing with iTunes. Whew!!
 
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