When flying in a fairly large vessel and when the atmospheric meter is completely on the left (no atmosphere) the throttle of the vessel starts resetting to zero every few seconds. You can throttle back up but after about eight seconds, the throttle will go to zero again. We have also noticed a tiny lag every time this happens.

Just when the needle hits 0 atm... throttle completely stops.

We have verified all ship parameters, fuel flow and everything but the throttle can only change when the pilot is actually pressing x, ctrl or shift so we compiled this down to a bug.

To me this has only happened once with the same vessel a friend of mine used, where he has this all the time and loses over 400m/s, which is quite substancial. We haven't found any other bug report with this problem for KSP and my friend builds huge space ships all the time in SP so I'm fairly sure that this has to do with DMP. My best guess is that some synchronisation event resets the throttle of a vessel that is actively under control.

I attach the craft, that is known to replicate this issue (SAS, First three stages and then let it fly until it escapes the atmosphere), to this issue: http://bloodisgood.org/ksp/ProjectLaytheBase001.craft

The setup we use is Debian Server with mono for the server and the issue appears to be very apparent when running the client on OSX, as I said, on my Windows, the throttle has only cut off once. This happens whether there are other players on the server or not.

Please let me know if there's anything else I can do to help find and solve this.

Is your server running any mods? Because I've seen this issue only on modded servers, never really seen on stock.

No this is pure stock ksp on server and clients.

This is TimeSyncer coming into play - We'll probably need to save and resume the flight control state if we pack the active vessel ;)