[Q] Protected apps and rooting?

Odd situation I have. I have a MZ604 Xoom which was rooted until I wanted to install HTK75D, and which point I screwed up the update and decided to do a completely fresh install starting from HWI69 and OTAing to the latest update. So I'm now running a completely stock MZ604, albeit with an unlocked boot loader, but 100% stock software. And for some reason a bunch of applications I did have installed while I was rooted are now no longer showing up in the Market. Through combination of talking to Google and a developer I've figured out that this is an issue with protected applications and a rooted device. However Google have now going into [somewhat typical] radio silence mode and the developers can't help me any further.

So my question is, why were protected applications no problem while I was rooted, but are now a problem since I've reverted to a non-rooted, non-custom stock ROM? And why will protected apps install on my unlocked, rooted, CM7 powered N1, but not on a stock Xoom that was once rooted?

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