The hydroboost offers more force than you can push with your foot, which is why the peddle goes down when the engine is running. I used to have that problem with my hydroboost. Its not the fault of the hydroboost, it is working correctly, as it is helping you push on the peddle. The most likely problem is the quality of the fluid. It is very likely turned to gel inside the reservoir. Time to complete flush the system and get the gel out of the bottom of the reservoir.
'83 Revcon Prince 31' FWD FMCA F298817
502 w/Howell/GM ECM/Edelbrock MPFI,Thorley's & Magnaflows, 4L85E 4 spd, KoniFSD