I'm having similar problems with the latest version of ebox-mail. I can't get mail server or virtual domain settings to stick. You're not alone, let's hope they fix it soon.
I does irritate me somewhat that responses on how to workaround such problems aren't forthcoming.
I built a new server based on 10.04 a month or so back and settled on EBox.
I didn't do my homework found out too late that it was beta and have spent (wasted) hours trying to work around bugs.
I'm still not sure where EBox keeps it's master settings, whether in file or database form. The /var/lib/ebox tree doesn't seem to be that place - i.e I manually change settings the GUI fails on but it doesn't pickup the manual change, but instead writes over the top of it.
I know it's a beta & I know its my fault for using it too soon.