I am having the same problem with apps that I moved using APP2SD Pro. I clear the market data and they come back only to be gone again the next day. I've seen this problem on this and the previous version of SS (5.4 and 5.5) across several version of the market app.
Same here, most days all apps will be there, but every once in awhile they will decide to disappear, clear data works, but I have another bug with apps showing they need to be updated when they are already fully updated.
Try the Market Tools in Titanium Backup to restore them. The other possibility which I've seen work when I've had this problem is to reinstall programs from the market.