While working with Migrate and Migrate 2.6 beta 1 I stumbled upon several undocumented "surprises" which are hopefully going to be documented, but so far, you can spend lots of time trying to figure out what may be wrong. Here's roundup of my findings:
1. There is one correct way of registering migrations and handlers
You should do this in hook_migrate_info(), your register code may look like this: