Rake definitions are stored as Preferences. Actual rakes are stored as part of a tournament.
So, I opened 2.5.12 and defined 2 rakes with custom names (like yours). I then opened the sample tournament, set the Per-player rake (both values, since I have 2 rakes defined), and the Fixed rake (again, both values). I then saved the tournament.
Then I opened 3.0. The 2 rake definitions with custom names were there (the preferences were successfully upgraded). I opened the tournament file and found that the rake values I set were there, too (the tournament file was successfully upgraded).
I never heard of a problem like this during the beta test. Are you certain the rakes have disappeared?