Looks like it's not re-seeding between rounds, that should be a simple fix.
The WSM-Liga champion getting a CHL spot doesn't seem to be consistent, though - I just ran a season and the winner (Slavia) was promoted to the Extraliga, but wasn't in the CHL; it was just the teams that should've been there. It may be some unusual set of circumstances that has to happen for it to occur; if you can upload your save (
instructions here) we'll try to figure out what went wrong.