Alright, so I've run into this issue several times before, and I still haven't found a solution which works for me.
Basically, I import my base mesh into Zbrush, sculpt away, but when it comes time to unwrap my level 1 mesh, everything goes to hell. After unwrapping, and I import the unwrapped level 1 mesh back into Zbrush, they sculpt explodes going up through the subdivision stack. I realize that this is an issue with the point order changing, but what's the workaround for this in Max and Maya? I'm using Zbrush 3.1, and this is a headache I'd like to cure once and for all. I know others have had the same issue as well.