Thanks, I do know the purpose of iExplorer I just wish Apple would include a setting that would essentially do the same thing.
I just noticed something interesting though and in my case, it may be what is causing the problem.
Earlier today my 'downloads' folder (on my computer - WinXP SP3) which is located at:
Documents & settings\user\my documents\my music\iTunes\iTunes Music had several files in it with the extension .sqlitedb. I didn't delete them as I was trying to figure out the process of what was happening during a sync.
As I had another error again today on my iPad, I synced both my iPad and my iPhone to iTunes over wifi, turned off wifi syncing and then closed iTunes. When I went to search for that same 'downloads' folder it was no longer there. I restarted iTunes and the folder was back but this time it was empty. So, that folder is created every time I start iTunes and gets deleted when I close iTunes.
Tonight I checked the app store on my iPad and iPhone and there were a few updates. I updated them without issue. When I opened iTunes (without connecting my iPad or my iPhone) I clicked on the apps tab and downloaded the updates to my computer instead of transferring them through a sync. I closed iTunes and since the downloads were successful no files were in the downloads folder when I restarted iTunes again. I then synced my iPad and iPhone again which went extremely fast. After each sync I checked the downloads folder which remained empty.
I am going to test to see if making sure the downloads folder is empty before syncing my iPad or iPhone solves the problem. If it isn't I will check and manually download any outstanding apps to my computer before syncing and see if that solves the problem.
Sorry for the long explanation and I know this sounds complicated but if updating the apps in iTunes serparately and then syncing solves this issue then I'm fine with that.
Hope this helps!