ITunes not recognizing my apps - saying I have 0 in iTunes, although the screenshots and memory bar clearly indicate that I do - what's going on?

Question

I have an iPhone 4s 16gb with the newest update. I downloaded a ringtone maker app for my phone, but apparently it's not compatible with the 4s - instead, it somehow messed up my whole system. I had to restore my phone to get the apps to open up, since most of them went into the splash page when I tried to open them but wouldn't actually open.
The restore was from after I downloaded the ringtone maker app, however. Now, iTunes doesn't recognize that I have any downloaded apps. And so, whenever I plug it into the computer to charge, it attempts to sync up but ends up messing my apps up so they won't open. I do that fix where I download a free app and then it works just fine, but there is still some kind of misconnection between my phone and iTunes.
Can anyone tell me what's going on?
See:
tl;dr - iTunes doesn't recognize my downloaded apps and messes them up when it syncs after plugin - why?

Answer 1

Hello R Hic,
I found an article that goes over how to restart and troubleshoot the Apple Mobile Device Service on Windows. I would recommend following the steps listed in that article and that should resolve your issue.
How to restart the Apple Mobile Device Service (AMDS) on Windows
http://support.apple.com/kb/TS1567
Hope that helps,
Griff W.