Probably sometimes your pistons' contacts 'bounce'. You could verify that by temporarily turning on the 'Log all MIDI messages ...' option on the 'General settings | General preferences | Advanced ...' screen tab, then looking in the activity log ('Help | View activity log') once the problem has next occurred. If there are two or more MIDI messages received from the piston in a row, when the piston was only pressed once, then that's the problem.
PCF wrote:HW auto detects my console's thumb/foot pistons (for the registration stepper) as 'Stop on hold-piston: MINI note-on/off'. 'Momentary piston ...' and 'Prevent rapid piston re-triggering' greyed out and cannot be enabled.
Since those particular pistons (+/-1, etc.) would never be lighted (i.e. are momentary/stateless) anyway, via the settings screen (right-click on them, 'Adjust ...') you could change their 'Input' type to 'Momentary piston: MIDI note-on' and then tick the 'Prevent rapid re-engaging (de-bounce)' option. Hauptwerk's software de-bouncing functionality is necessarily basic, but it might be enough to stop the problem.
If your pistons' MIDI encoder circuitry has hardware de-bouncing functionality (maybe configurable via jumpers on the circuit board, or similar) then that would be the ideal option.