This generally happens during the photoperiod, in any kind of set-up. In low light set ups, to many water changes, causing fluctuating C02 levels can 'exacerbate' black brush algae. The causes of algae will always be light and ammonia, what people seem to forget that there is always some ammonia traces in the tanks, if there wasn't our filter would die. In high tech it can be problems with diffusion, again it will normally end with BBA.
In a low tech set up, the best time to do a water change is at lights out, this gives time for excess C02 to 'gass off'. It remains a little more difficult in a high tech set up. You need to crack the best diffusion method from the beginning. It has been tried and tested that the best thing to do is to have the C02 set on a timer to come on 2 hours before lights on and finish an hour before lights off. Most aquatic plant scientists will agree that the most important part of the photoperiod is the first 2-4 hours, this is where most problems occur as this is where the plants will use most C02, N and P etc etc.
hope this makes some sense.