Now I know a lot of people are saying that Silicates have nothing todo with Diatoms but even so..
I'm not one of these people. I've seen some compelling evidence that sometimes silicates can be high enough to cause diatom blooms that never go away. Saltwater hobbyists even deliberately add sodium silicate, to create controlled diatom blooms as food for their critters.
Rocks, gravel, and sand usually release an initial burst of silicates, which tapers off with time; leading to "new tank" diatoms. If you reuse these from a previous tank, even if dried and let sit for months or years, the initial diatom bloom is typically smaller or even absent.
Of course, a poor tank setup, sudden changes, or overfeeding can also induce and extend diatom blooms.
But even if none of the above are a factor, if you have a continuous source of high silicates, the diatoms will just hang around.
You already know about the silicates in your water, which you've reduced by using 50% RO water. And reduced the overall amount of diatoms in the process. Where are they still growing? On the rocks. They're releasing additional silicates, and between that and the silicates in your remaining tapwater, it's enough to trigger a limited bloom at the point where concentration is highest.
If you go to 75-100% RO, it may be enough to keep the silicates from your rocks from being an issue. Or you might get rid of the rocks. Or use an adsorbing resin, though this will adsorb phosphates as well.