That sounds like the equivalent of a 'short circuit'. Something is open when it shouldn't be, so the 21 MPA from Pump 2 is leaking into the Pump 1 side. Maybe.

Can you use dye to trace leaks through valves?

(Beware that such issues often turn out to be something that you didn't describe.)

why "aircraft" forum ? why not "mechanical" ?

another day in paradise, or is paradise one day closer ?

This should be posted in the fluid power forum and would get more relevant traffic there, so hopefully it can be moved.

Can you post a schematic? Without one we're just guessing and can't help you nearly as well.

If the lines from each pump to the cylinder are common, with no valving to isolate them, then they will have the same pressure in them. Is there something that is supposed to isolate the pumps from each other?

The other thing to keep in mind is that piston pumps are positive displacement pumps, and as such will deliver the same flow rate regardless of how high the pressure rises, until one of a few things happen (depending on how the system is configured): a relief valve opens to vent excess flow, thereby limiting the pressure; the pump destrokes to limit the flow and/or pressure (this applies only to variable piston pumps); something fails (motor stall, shear coupling slips, pump internals break etc). Note that the last one should never happen, but sometimes things don't operate as intended.