Any ROM (factory or home-cooked) has a signature or footprint attached to it. Google has a list of "valid" signatures. If you ever log into the market using a ROM with a signature Google has not flagged as valid, protected apps will not show. It's part of the anti-piracy measures. Your market account gets flagged, and you're stuck. There's two ways to remedy it -
Google purges certain signatures from their database, then flags the offending signatures as valid. Next time you log into the market Google's info about your account is updated and you're good again.
You flash to a ROM with a signature from "official test builds" (ROM built from source for a development phone) and Google see's (thinks) you have a dev phone and purges your server side cache.
Since the Eris isn't rooted yet, you're going to have to let Vzw and Google fight it out. If by chance it gets rooted soon and before they straighten it out, I can help.
Why an official updated signature is not flagged as valid is a clusterf* that I have no answers for

Same thing happened with the first Sprint MR, and still happens to anyone who tries out a 2.1 test build.
@Jeremy -
There's an easy way non-rooted phones can back up their protected apps. Is it OK for me to post how it's done?