The air bubbles. The valves are designed to operate under hydraulic fluid pressure. You're making them operate with air which compresses under pressure. Besides shifting problems, that fluid puts pressure on the pistons that apply the clutch packs. Air in those clutch packs prevents sufficient pressure holding the clutch plates together so they will slip. That leads to rapid wear and overheating.
The air is coming from the fluid being whipped up by rotating drums. Suck out enough fluid to get the level to where it should be. Let it sit for a while for the air bubbles to work their way out.