Itunes Says and Looks Like Syncing But isn't..help please?

Hi,
Not had my ipad too long but had some issues syncing itunes (and now aps) from my windows 7 pc. I downloaded a number of aps (both paid and free ones) onto my ipad. Over the weekend I tried to sync my itunes to my ipad. It shows syncing and shows all my music being synced across. Except it hasn't synced it across and has now removed all aps onto my pc. I tried to update the ipad os to the last 4.2 and have also tried restoring the ipad without joy.
What am I doing wrong please?

Thanks,
Rich