I have this same problem, but after hours of trying make it to work, I think it has nothing to do with G53/G54 coordinate systems nor G90/G91.
In my case, probe cycle works perfectly the first time (after reset or boot) but in subsequent probe attempts, z moves Up instead of down.
What I have found is that the input pin (in my case di5) used for probe (zmin) stuck in true (latch) after the first probe cycle, so in the next attempt g2 reads the probe (di5) as active, so it just skips the cycle and retract (z up movement).
The only way to restore di5 to false is to reset or tap the probe manually few times until it change. After this, the probe cycle works again one time.
I have confirmed that the latch is not a mechanical problem, the voltage read at pin di5 is 3.3v but g2 read it as active. (it is configured as NO so 3.3v is NOT_ACTIVE and 0v is ACTIVE)
I have read somewhere that someone reports the same behavior but I could’n find the source again.
