I don't know if this phenomena translates into PS3 locos, but when I had this happen sometimes on several P2 engines, I realized at one point (for at least one engine with the problem) it was more prevalent if I was not feeding the track a full 18volts. (i.e., I saw the problem, realized the voltage wasn't all the way up, powered down everything and when I powered back up I dialed the voltage higher and the problem then disappeared)
Are you using bricks (or a TIU on a fixed voltage channel, etc), or are you feeding the track directly with something that is adjustable?
May not be your issue, but it's something to give a quick try, if you are using transformer handles or variable channels to feed the track.
There are quite a few old posts on odometer readings, but most were I think from before P3 came out.
-Dave