What sort of separations are you using? For the life of me I can't get isolated, stand-out colors using RGB separations, and have much better luck with CMYK.
I primarily use CMY seperations made from the channels pallet. Creating CMYK produces completely different negatives.
DaveC I get intense reds when I need them doing bi-color gum over cyanotype.
I use Quinacridone Rose as the last layer. The M. Graham and Daniel Smith brands of this pigment work very well. 1 coat for the yellow and 1 coat for the magenta layer. You are going to hate me for saying this but you need to size your paper. I use a very thin watery layer for the magenta coat. You do not need to put alcohol into the pigment mix. Though I do use grain alcohol with my gelatin size to kill the sparkles.
I use FAEW and Rives BFK papers. With FAEW I print on the mesh side, though after double shrinking and sizing with 3% gelatin and hardening with 2.5% glut the surface is soft and smooth as a babies butt. I really prefer BFK.
And I also use a dremel tool to mix my pigment mixtures and my coating mixtures which uses saturated AD. I brush on the mixed coatings with a very slighly dampened very high quality hake brush followed by a even and light roll out with a micro-foam roller. Almost all magenta pigs cause oily mixtures which are plaqued with fish eyes. I do the final smoothing with a large badger hair brush once the surface gets just slightly dry to rid the coating of those. The badger hair brush works the magic.
I forget how you are creating your negatives but I use PDN and create an individual adjustment curve for each pigment, including the cyanotype layer. By doing this and using CMY negs. the color is placed very precisely in the print. An alternative which I will explore soon is to also use an ICC profile when working with the positive image before color seperation. This will aid in softproofing if you understand how to do that properly.
I develop my prints for 1 hour @ 70F. Often I will have to use a water atomizer to get the final layer of magenta to release. This provises a very fine mist of water to develop the pigment and help it release. If I find the magenta (or yellow not releasing) I'll develop in warmer water for a short period to get the development started. Of course brush development is needed in some areas just to clean out whites or intensify certain colors, but that's an advanced technique that requires finesse and practice.
Be gentle handling the prints while they face down. If you let them plop strongly in the water the magenta layer may just slough off from the shock wave created to the impact. A wave front reflects off the bottom of the tray and scrubs the surface of the print.
If you are familiar with the Adobe Ole Moire file, print that in gum until you have a perfect tri-color print as you can make it. It will teach you a lot.
Using cyanotype as the Prussian Blue layer reduces the color gamut and you find certain colors impossible to match or create in the green, blue, aqua hues if that is your goal. Using the Adobe file mentioned above will help you key in on reproduction of flesh tones.
I don't know about flocculation but I just call it staining which is what you've got.
Good luck,
Don Bryant