iPhone 4 doesn't auto-sync, manual sync doesn't pull up any apps

So this is a pretty common problem and I'm going to try to find my other charger as one solution, but my whole problem doesn't completely match what other people are experiencing.

I recently replaced a 2008 MBP with a brand new one with Mountain Lion pre-loaded (I haven't updated to Maverick yet because I'm having enough trouble as it is). I have, as the subject line stated, an iPhone 4. I've never had a moment of trouble syncing, but this time I can't do it.

Here's what happened--I was charging my iPhone and got the message that iTunes needed to be updated. I cancelled that message, but immediately got the desktop notification that the App Store had new iOS updates. When I checked it out, one was iTunes, so I clicked on the iOS and the iTunes updates. I eschew Safari, so I never update it, and I don't use Remote Desktop so I left that one out as well.

When the update was finished and my computer restarted, iTunes started right up because my phone was still charging, but it didn't sync. I had just purchased a new app, so I went into the apps tab in my phone sync page on iTunes and, while I could see the graphic of all the pages with apps on them, only my single newly purchased app was in the iTunes list. I attempted a manual sync, but literally nothing happened.

My problem, then, as you can no doubt see, is that not only are the apps on the phone not syncing properly, but none of the other apps belonging to that account are pulling up. One recommendation to go to File>Devices>Transfer Purchases from iPhone ONLY transfered what was currently installed on the phone. Where are the rest of my apps?

I've had 4 different computers since I got my first iPod touch in 2006 and not once have I ever had this kind of problem with iTunes. What the heck is going on?Do you think updating Safari will help with any of this (I know we are forced to keep it on our computers to make iTunes go)?