Checking anything in Advanced overwrites ALL info on the iPhone with what is on the Mac or PC.
This is not something you want to do if you manually put in allot of Data as this would be overwritten.
Your best method would be to go to iTunes Preferences in Windows- iPhone Tab- Reset Sync history and try and sync again.
or on a Mac open iSync in Applications. Then open iSync Preferences and Reset Sync History and test again.
iPhone: Syncing and merging data
http://docs.info.apple.com/article.html?artnum=306071