From someone I trust:

MGR only counts when the tournament entry fee is paid in the form of cash from your account. So, if you play a Step 5 $1000 + $65 SnG directly, then it would be counted. If you qualified from Step 1, then MGR is only counted for the $10 + 1 Step 1 game because that would be the only one you paid cash to enter.

PS- I could use a little help working on a new reward scheme for Party, PM me if you would like to help test the system.