Sync apps are different on my computer from my iPhone

We have 3 iPod's and my iPhone. The apps on my computer are different than the ones on my iPhone. They are a combination of the wife's and both my sons apps. If I click on SYNC APPS, it tells me that all apps on the iPhone will be lost.
How can I fix this? Do I need to delete iTunes and reinstall it?

Which apps?  Where are you downloading from?  Which browser?  Version?
Please detail ALL you have done so far in the way of troubleshooting?   Need this info to avoid the been there done that scenarios.
You provided no system details. 
When posting in Apple Communties/Forums/Message Boards.......It would help us to know which Macbook Pro model you have, which OS & version you're using, how much RAM, etc. You can have this info displayed on the bottom of every post by completing your system profile and filling in the information asked for.
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