I assume you are running these engines using TMCC or Legacy. Is the command base's 3-prong power supply plugged directly into a properly-grounded wall outlet? If the command base is plugged into a power strip, does that strip have surge protection? Many such power strips interfere with the TMCC/Legacy signal transmission and will cause the type of intermittent problems you're seeing. Replacing the premium surge protected power strip with a cheapie strip with no surge protection can fix the problems.
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