Hey guys, found out the problem. I just recently reinstalled windows, and iTunes saw in the xml file that all my apps were there, but it didn't know their exact location. So I manually re-added the apps to iTunes by going to "Add Folder To Library" and now it works perfectly.
Thanks for your help anyway.
And chobbs, I did notice also that my phone runs faster when it's not restored from backup.. When I activated it yesterday I was kind of underwhelmed by performance but I didn't think it was unusual. It's definitely better now!
Sidenote: iBooks still takes a hilariously long time to open compared to other apps.. :P