Oh cool, I wasn't going crazy. I just downloaded the beta server files two days ago, and I had this same issue on my testbed. I just couldn't get the client to join.
After a little bit of review, I just needed to manually update the server mods to whatever the client was downloading (build 227 for each, iirc). Once I did that, everything went up smoothly.
My whole reason for upgrading early is actually pretty funny: Dimension Doors broke, and I could not get it fixed for the life of me. Even a clean install of the mod would complain about mismatched IDs. I knew that the newer versions of DimDoors were using a slightly different file structure... but didn't know anything beyond that. Figured that if they use a different file structure, they MIGHT have a robust recovery and conversion system that would allow my doors in the Overworld to exist without the mod complaining. Turns out my gut was right.
We don't have anyone with an established base on the Moon or Mars, so we haven't run into any airlock glitches yet. I can't wait to get Hell from my players when they realize there are problems. >.>