PEC is a bit of a dark art in EQMOD. It doesn't work at all on my EQ8, but that may be something to do with the mount software - but how to tell?
In partial/possible answer to your questions, when messing around with PEC on my EQ8, it got into a state where tracking was not working and whatever was screwy was being stored somewhere to mess up future sessions (again, who knows what it was storing and where). I had to reinstall both PHD2 and EQMOD to restore it to normal operation - if all else fails, give that a try.
The other thing is that EQMOD will occasionally boot up with a Northern Hemisphere site location (or sometimes not at all). Easily fixed with a restore in the config section of the toolbox (provided that you have a saved config file in the first place).
But, minor irritations aside, it is still great software - I can't imagine going back to the handset.
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