Had the same issue with my 29 cube. Here is what worked for me. If you have algae then you have a phosphate and/or Nitrate issue. First, make sure your Nitrates are very low. Make sure your using RODI water with 0 TDS. Not sure how much you feed, but cut your feeding. I currently have 3 fish and only feed 1/4 to 1/8 of a cube of frozen a day. You can get a Hanna Checker, but this will only tell you how much "free" phosphate you have in the system. I use mine about once a month. I usually just look at my tank, if there is more algae, then I have a nutrient problem. get a good mix of snails for a clean up crew. Put a skimmer in your second chamber and skim wet. Your rocks are probably leaching phosphate out, so depending how long you have been set up and how much phosphate they have, it may take weeks or months to get the excess phosphates out of the system. I used GFO in the past, but I'm not sure how much it helped. I feel good house keeping is the key. I also use a turkey baster to blow of my rocks occasionally. When I had algae I did it once a day, now about once every couple of weeks. Until then, keep scrub the rocks with a tooth brush and cleaning/changing filter pads out regularly. FYI: I got the media basket insert from In Tank and use pillow stuffing instead of filter pads. much cheaper.
Like everything else in reefing, time and consistency are the key to beat this.
David