The PR4 is a programmer, not a command station, and therefore isn't intended to run a loco or test a decoder's functions (the very limited exception being certain Digitrax sound decoders).
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As you have found, trying to use it in a manner for which it was not designed may produce inconsistent results. It has long been my contention that the JMRI throttle be disabled when using a PR4 (or a PR3) in stand-alone programming mode.
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Steve
"Breezlys"
