Hmmm...sounds like you may have to uninstall iTunes and reinstall it. This will NOT affect your library.
You need to uninstall all Apple programs from your computer...Apple Mobile Device Support, Apple Software Update, Bonjour, iTunes, and Quicktime.
Before you do that, something just crossed my mind...How are you syncing? Is your USB cable plugged DIRECTLY into your computer or are you using a Hub? You must be plugged directly into your computer, do not use a hub. Also try changing ports. IF this does not work then do the above and reinstall it from the iTunes store.
If reinstalling iTunes does not work then you may have to restore your iPhone.
RESTORE IPHONE:
Step-by-Step
1) Close all programs and restart computer.
2) Open iTunes and plug in powered off iPhone with direct USB connection.
3) If iTunes fails to connect to iPhone...continue to #4, if it does...restore.
4) Shut DOWN iTunes again.
5) Power OFF the iPhone & Disconnect from computer. (Power off two ways-one will work, hold home and sleep button until off or just hold sleep button until off)
6) Hold down Home button & connect to computer using direct connected USB cable (keep holding down the home button until iTunes sees it).
7) It should go into recovery mode and iTunes should recognise it.
8) If you want to recover to previous software version, Hold Alt/Shift and click restore in iTunes. Then select the old update version.
DFU MODE:
Step-by-Step
1. Turn the iPhone ON
2. CONNECT it to the computer with a DIRECT USB connection.
3. Make sure iTunes is open so you'll know when it enters DFU mode.
4. HOLD the Power/Sleep-Wake button AND the Home button for 10 seconds.
5. RELEASE only the Power/Sleep-Wake button and continue to hold the Home button.
6. WAIT until iTunes recognizes the phone in DFU Restore mode (in Windows a bubble pops up saying it recognized new hardware "DFU Mode" or something to that effect)
The last step may take SOME TIME, like, say, even 60 seconds or so.
The screen should be OFF (black), if you see the "Connect to iTunes" logo, START OVER.
It may take a few tries to do the steps just right, just reboot
(hold both Power/Sleep-Wake AND Home until the Apple logo appears and the phone turns back on) then try again.
7. Then restore the iphone
-Plug one end of the cord into your phone and the other in your computer
-Remove the cord in your computer, leaving the cord in the phone still plugged in
-Hold both the home button and on/off button on the phone
-Once the screen turns off, let go of the on/off button but continue holding the home button
-Plug in the other end of the cord in your computer while still holding the home button on the phone
-Once the apple logo appears, continue holding until you see the plug into itunes screen on your phone
-Click restore.