I think this has been discussed before, have no idea where - probably in the km that contains the beginnings of the Vuo 2.0 redesign.
The reason for the colors being what they are is that they are compatible with the Brewer color scheme for color blindness iirc. I think one of the options that came out from the discussion was that there could be a possibility to create your own color scheme and so on - but it might be me misremembering as well. Composition notes will solve a lot of the organising challenges though.
but both are in separate windows and should be handling the frame rates independently, right???
Maaaaaybe? I'm not too sure about it to say the least. Have you had open the Desktop Video setup window while looking at the issue? It might be that the driver wants to lock down everything to the same framerate. Using their mixers locks everything in the chain to the same framerate, but I don't know if this is transferrable to the desktop video products (I'd assume so since it is the same driver). 30 and 29.97 might be so close that you get partial delivery anyways, but then drops out when out of sync.
Looking at the camera specs, it seems that you should be able to switch both to 1080p 25fps. Can you try that and see if you have the same issue?