I strangely didn't hear anything about it when they were last fixed, but for a long time I've been able to keep my Achievement progress. The issue seems to have returned as of 3F, and I've consistently noticed problems with my Achievments being reset and/or rolled back.

... Although I'm not sure if this is actually intended, what with the stat wipe that the devs are doing prior to release...?

EDIT: I'm not in any way certain, but I begin to wonder if this problem may be tied specifically to the act of playing Custom games. I recently played a long string of Pantheon matches without a problem, but after having played a single Custom game, my achievements were wiped clean once again.