The new membrane shouldn't have to "break in." It should be producing water (the right amount!) right away, and then you just let it run for a while (I run mine for an hour or two right away) to let any chemicals or whatever get out of there before you start using the water for your tank.
I'm not one of the RO/DI experts on here, but I know it should've started producing the right quantity of water right off the bad. I'm sure others can help you get it back up and running correctly.
-Joe