I did my transfer about 4 weeks ago. My JBJ nano was a cyano farm. (reasons are not important now)
Phosphate bonds to rock and sand. Thats important to remember.
I took my sand and rinsed the heck out of it to get the solids and dissolved organics out as best I could. I dipped several, most actually of the rock in a peroxide salt water rinse before putting them back in the tank to zap as much pest algae as I could and remove excess organics and nutrients.
I had 2 rocks,one with tiny polyps a friend gave me that was a cyano convention center(PO Bound Bomb), and another Id had doing much the same.
Once everything was in the tank, I turned on the new lights and the cyano started immediately, esp on the 2 cyano bombs.
The new lights have a much better spectrum and higher intensity so I set them at the same intensity as the old lights and began the light acclimation Estimating about 2 weeks. I also added a refugium with 6 different macros and an intense light.
Over the course of those first 2 weeks the cyano bloomed in the first several days, but during that time my corraline began to grow every where pretty quickly and the fuge I had to trim on week 2.
In the first week I could literally watch the cyano recede on the 2 bombs. Any other nuisance algaes lasted a few days only and we mainly on the glass and I actually left the back glass alone to grow(and remove more excess nutrients for me that I scraped off, sent to the filter and got out by water change)
I continued every day to blow as much dust into the water to be pulled out by the filters. The only algae was on the glass and the cyano was gone completely.
I have to assume I had pulled the PO off the rock and into the mouths of the ones I want to feed it to.
Now at week 4 The cyano is back, guess where, on the sandbed naturally as now its had time to stew. I believe that I had maxed out my natural po removal methods, and as theres a lot of sand(po bound) , so now Ive augmented my PO removal by adding GFO. One teaspoon on day one.
That brings me to today. Cyano has made no progress but has not gone. I need to clean the front glass every other day really. The back glass(I call it my snail feeder) is still a bit funky but manageable. My corraline growth has slowed so Im not going to continue adding any more Po removal and its likely I remove the GFO in a week or so.
Not that it matters, but the only thing Ive dosed is Prime and Fiji mud.
So what Im guessing is you didn't get enough of the organics off the rocks and sand during the transfer. So now theyre free to wreak havoc in the tank. And depending on how long they take to break down into PO or NO is what is causing the Phases. That plus the amount of Po bound to the rock and sand.
So the long and short, remove as much dissolved and particulate organics as you can manually and mechanically.
Slowly reduce the Po in the tank by giving it competitors and if its still advancing GFO.
Ya might have to deep clean again or not. Gauge that on how bad you think it is and if you can pull it out without rebuilding.
Im pretty happy with whats going on in my tank right now, I got the tips and a much better understanding of these processes in the last few months by reading and conversing With Randy Farley, twillard and brandon429
Check out the Pest algae Challenge thread.
https://www.reef2reef.com/threads/reef2reef-pest-algae-challenge-thread-hydrogen-peroxide.187042/
And reread some of Randy's articles.