I also have WHM, and whether having the two networks under separate cPanel accounts has anything to do with the problems I'm not sure.
I only want the users, and I tried the User Import and Export by Waindigo, but it really failed. I've been at this for five hours now, and I've searched for ways to do it, but I really can't find it. To MyBB I moved the community from Ning, and due to the major difference in the software, I lost many members (over 3000).
I really don't want to do this by hand, but I can if I have to. Because of the original move, the community now has about 800 members, but again, I really don't want to do this by hand if there is another way.