I've been away for a while, so in case you are still listening...
You have discovered a "feature" in the PMDX-126's charge pump operation that apparently isn't mentioned in the PMDX-126 manual. When the PMDX-126 DIP switches are configured for "normal mode WITH charge pump", if the E-Stop input goes active, then PMDX-126 requires the charge pump to stop before the PMDX-126 will de-assert its EStop on parallel port pin 10 (as you discovered), even if the EStop input to the PMDX-126 is grounded again. The charge pump stopping acts as an acknowledgement from the PC to the PMDX-126 that the PC "saw" the EStop signal on pin 10.