When the fills are grayed, visit the ‘Advanced’ tab of that layer in the ‘Cut Settings Editor’ to see if you have ‘Flood Fill’ enabled. When on, Flood Fill will take precedence over any other filling option.
I am not seeing what you describe. Here I show two layers, one is black with circle shapes set to ‘Fill groups together’. I have 10 circles, 5 of which are grouped. The second layer, red, is set to ‘Flood Fill’ and also has ‘Fill groups together’ set. My output shows both layers producing as expected, the grouping for the black layer is produced in one go, followed by the other 5 circles producing one at a time. The red layer is producing the Flood Fill. We grayed the fill options in our recent releases when Flood Fill is set, to help eliminate confusion moving forward.