I have the same boat, same year, same problem. It's usually a prime issue. When I encounter this I run the boat at planing speed and turn the pumps on and we are good to go. Very similar to whats happening when you open the valves at speed. Have you tried it this way? Can you hear your pumps working?
My research online along with extensive discussions with Jason @ Wakemakers convinced me that it's time to scrap the Supra system and install new pumps & intakes for each bag. Many others have done it with great success and will eliminate the issues inherant with the factory system. If you use your ballast system as much as we do ours, it seemed like the thing to do. I just want it to work every time, and fill/empty as fast as possible.
2007 Supra Launch 22SSV
(2) Wetsounds Rev 10's, (6) XS-650, (1) Syn 6, (1) Syn 4, (1) Kicker 10" Sub, WS-420SQ Full RGB LED on Wetsounds
(2) SeaBlaze 3 Blue Transom Lights
Supra Surf swim platform
NauticLogic GPS Speedwheel/Perfect Pass Interface
Wakemakers Ballast Upgrade, 3 Pump Fill, 3 Pump Drain