Painting dark colours on white.... You might need to paint more thickly to cover it. The acrylic stain might also have been preventing the gesso from soaking up the oil from the paint. Those are my only ideas. You should not have to go back over everything at all
Instead of using that watercolour brush, I've found the Rosemary Ivory brushes to be just as good. They're really soft and nice. I only have a #3 filbert but would like to get some more of these ones... soft hairs but are still fairly firm and have nice spring to them.