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Are you using an EQDIRECT cable, or going via the handset in PC-Direct mode? It's weird that you can slew manually (using the direction buttons) on both axes in EQMOD, but that pulse guiding is not working on at least one. You didn't accidentally set the minimum pulse durations in EQMOD as too long? Given that it's the same issue in whatever guiding software, and was fine for ST-4, I'm strongly suspecting an awry pulse-guide setting in EQMOD.
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