ITunes won't sync to iPhone 3GS, iTunes appears to be wrong version?

OK this is really weird, my dad updated to iTunes 9.0.3 last night and his iPhone to OS 3.1.3, I confirmed this by checking Installed Updates under Software Updates in System Preferences. Software Update also says that the system is up to date.
If I go to iTunes > About, the version shows 9.0.1, even after I have re-downloaded iTunes 9.0.3 from Apple.com and installed it successfully, it still shows 9.0.1!
It was working fine for him before the update, now it won't let him sync anything to his iPhone (except e-mail, contacts etc...). With apps it says they are not authorised and it removes the icon from the iPhone page (the virtual one in iTunes that let's you position your apps where you want them), with his songs/podcasts they get sync'd, it shows up as 76MB music in iTunes that's been sync'd to it. But I went to the iPod app and it says there is no content there.
I just deleted something called the "SC" folder, and it when I went to Store > Authorise computer, it says "You already have two computers authorised including this one". So just now I tried to sync an app on the freshly restored iPhone, and it says "iTunes can't sync these apps to your iPhone because your computer is not authorised".
Soo, does anyone have any suggestions?
EDIT 1: I updated my iTunes and iPhone OS 3.1.3 before he did and mine is working fine.
EDIT 2: It seems I can sync Photos just fine, I've tried one podcast, and a normal playlist (not a smart playlist) without success, it shows on the capacity bar that I have 1.19GB audio (in blue), ~180MB photos (in yellow) and ~196MB of other (in orange) and FREE is at 27.78GB.
EDIT 3: In the iPhone under Settings > General > About, it shows 0 songs sync'd which is wrong, but shows the correct amount of photos (280).

It appears to be fixed, he had multiple versions of iTunes installed (since he put his iTunes in a different folder) the iTunes icon launched the old iTunes, even though the new was installed. it's working now.

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