shorty , with a new system, or a move from one system to another, you're always going to have a cycle, whether that is detectable or not. There is a die-off and recolonization of bacterial and periphyton (sponges, etc) whenever you move rocks or change flow. So what you are seeing is in many cases unavoidable. Time will balance things out. I wish I could say "your scrubber will fix it" but that's just not necessarily true. Maintaining consistent water parameters (alk cal mag, etc) is what is critical to stability long term. Algae/cyano in the tank seem to take advantage of instability.
The yellowing of the water is typically a result of not cleaning the screen early enough - the roots/base of the algae mat starts to die, and then releases it's stored nutrients into the water.
I've been running one of 3 different versions of scrubbers for over 2 years now and no yellow water in sight - and I just did a PWC a few weeks back (first in a year) and the water was crystal clear in a white bucket. Poured it in the toilet and it looked as if I had just flushed - clear. So that tells me that something might be missing in your construction or maintenance of the scrubber.
Instead of running GFO, you might want to test your Potassium and dose that if it is too low. Salifert makes a good kit, easy to use, relatively accurate. Boost K and your algae growth can get better, P will drop (because the algae could be limited in growth by deficient K) and corals will like it as well. 390-410 is where you want it.
Some people are reporting that running a skimmer can actually contribute to scrubber growth, because the added CO2 and O2 just from the skimmer pump can aid in keeping Alk in range, as algae will suck all the CO2 out of the water then go after carbonate (or is it bicarbonate, my mind is not functioning today) which drops Alk faster than normal. Also you can run a skimmer pump (needlewheel) to feed the scrubber, or get air injected into the flow to the scrubber to help balance alk uptake (or rather to reduce it)
All that being said, there are some that ore of the school of thought that there should be some N and P available in the system. I have heard speakers state that they prefer to keep N around 10 and P around 0.02 actually. I don't know if I believe that or not, but I've heard it from more than one person.