@Tcdasa: Then, yes, Calibre does help with this (by uploading the thumbnail itself, to workaround a quirk in the Touch's behaviour). This sometimes confuses the Touch if you happen to update an existing item, or deleted an item manually (ie. not from the Touch UI), especially if the item has broken/inconsistent metadata.
This Calibre patch
is related, but doesn't help on the Touch if an ASIN is set. It simply more closely matches what KG does.
As thomass said, make sure you're using a recent enough Calibre build.
And it indeed has nothing to do with JBPatch
(@ixtab: Unless the cover workaround for files with a non-amazon ASIN in the Cover View patches has a wider reach?).