CTC GC-PAL issue with MSD Chemstation

Running an Agilent GC/MS system (6890/5975, MSD Chemstation with CTC control add-on) with GC-PAL autosampler. Been running for years with no major issues. Last week, the helium ran out and so the sampler was stuck in the "waiting for ready". Changed cylinder, reset everything and now the CTC gets the command to start the injection, waits for system ready, injects the sample, sends the remote signal to the GC/MS to start the run but then... it just stays there at the GC inlet instead of going on with its usual cycle of cleaning and going home until the next injection? CTC Status message in MSD Chemstation just stays at "RUNNING - Injecting into GC Inj1". AFter the method has finished running, the CTC then no longer responds (if I try to reset the injector through MSD Chemstation, it's saying it reset it but it clearly did not, or the software just freezes). Now, if I try to run a method outside of the software through the CTC control pad, it runs as expected.

It's very odd because according to the CTC manual, after injection and sending the remote signal, the autosampler should not be waiting for any reply/sync signal back at this point...

I have tried pretty much everything I can think of! Full cold boots, changing the COM port, different method, configuring a new GC/MS instrument in the MSD software, different cables for both the serial/USB connection and the remote cable, running with GC only configuration (no MS), resetting defaults in the injection method, selecting a different injection method from those available, reflashing the CTC with an older backup .sss file, as well as removing and re-installing the Agilent control for CTC software... NOTHING WORKS.

If anyone has come across a similar issue or has ANY idea of what I should be looking at, it would be greatly appreciated as I'm at a complete loss after several hours.

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