Oh, wow, ok. It looks like you're using plywood for your side panels. the natural grain of wood has different densities in different areas. I.E if you have a piece of plywood faced with pine, the dark areas of grain are much harder due to more resin content, and will not sand down as fast as the light areas. Therefore, if you sand you have to use a sanding block or hard pad, to stay flat rather than follow the contours, so the softer areas are bridged over and you keep a flat surface.
In your case, if I'm reading the pic right, you've sanded valley's into the softer areas of wood. Or, the Zinnsers maybe raised areas of grain? (moisture in the finish can cause areas of wood fiber to expand or stick out, usually only an issue with water based finishes)
If you can do it without sanding through the top layer of wood on the plywood, you need to sand back to flat with a stiff sanding block and coarse grit paper, then sand back to the smoothness you want. then go back to painting. If any of this isn't clear let me know. I've finished a lot of cabinets, doors, etc. both with paint and stains.