3rd generation iPod touch syncing issues

The last time I tried to sync my iTunes account through a wired connection between my Macbook Pro and 3rd generation iPod touch, I had some major issues.
First: It deleted the YouTube, iBooks, Netflix, Dropbox, Facebook, and Kindle apps from my iPod and will not let me reinstall them because they are "not compatible with this iPod." This is really annoying.  It means I can never sync my computer with my iPod again.  The only way I can get those apps on my iPod is if I go to the store in the iPod and download each one individually.
Second: Some songs that I have recently acquired will not sync with my iPod because they are not the right format or something.  I never had issues with this before.  This song is in the same format as some songs I aready have on the iPod.
Solutions I have tried:  I tried reinstalling iTunes and it didn't help.  I tried reseting my iPod to factory settings and starting with a "new iPod," twice.  This did not help either.
My Question: Is this an issue because my iPod is out of date and means that I am just SOL or can it be fixed?

The shuffle and iPod touch use different drivers.
See:
iOS: Device not recognized in iTunes for Windows
I would start with:
Removing and Reinstalling iTunes, QuickTime, and other software components for Windows XP

Similar Messages

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    Verify that all play in iTunes on the computer.
    Then
    Removing and Reinstalling iTunes, QuickTime, and other software components for Windows XP
    or                     
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    To delete all music go to Settings>General>Usage>Storage>Music>Tap edit in upper right and then tap the minus sign by All Music
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