Problems syncing iPad photos and Aperture

I think my iPod Photo database is corrupting for some reason as I keep getting intermittent problems syncing photos from Aperture across to my iPad.
Running Lion 10.7 on a Mac Mini with Aperture 3.1.3 and each time I get the error if I delete the iPod Photo folder it will do a full resync the next time I connect, but with over 5000 photos it takes some time.
Anyone had a similar problem or know why it might be doing it?
Thanks

From your words "syncing with my old iMac" it appears that you are now syncing to a different computer. What might work for directly imported photos (emailed, CCK, screen shots) is to connect your iPad to your new computer and right click on the iPad in the left part of iTunes and select the backup option. When that is complete then you right click and select transfer purchases. Then let iTunes erase the Ipad and replace it with the contents of iTunes on the new computer and then restore from backup
Photos synced to the iPad are not included in the backup and those will be lost unless you can get them from your original computer. However, there may be some third-part computer programs that can get the synced photos off the iPad.
For what are in backups see:
http://support.apple.com/kb/HT4079

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