DrLicor, thanks for the response. I've been trying as you suggest since. However, the problem seems to not be associated with the speed/incidence of warp spamming or otherwise... Rather, it seems to be associated with moving certain ships around on a career save, and it especially happens in low orbit. For example, after an aerobrake maneuver, I'll set a maneuver node at 0.0m/s to mark a spot for Kerbal Alarm Clock... and the m/s creeps up for that node, independently - in vacuum with all engines off.
Any ideas would be really appreciated, as it's killing this save file for me!