Thomas:
I just had a quick look at your log files. I need to spend some more time looking at the logs; but, these two events suggest something is odd with your ignition.
At 53.3 seconds
At 133.4 seconds
The white trace on each lower graph is your base ignition advance. Engine speed and MAP are changing small amounts; but, your base ignition timing is going through rapid swings greater than 10 deg. Do you have a very sharp change in your ignition map around 900 RPM? I looked at other places on the log with similar RPMs and MAP values and I didn't see similar movement in the ignition advance (I scanned the log quickly so I could have missed things).
I don't know whether this variation in the ignition timing is what is causing your problem; but, it is something that you should check out. I also note that your TPS is reading -4% (presumably closed). I don't think that would cause your problem; but, it can create some problems with the throttle cut depending on what settings you have for throttle cut. I try to program mine to give 0 to 1% closed and around 99% fully open. There are some rounding off things that occur in MSExtra with the A to D converters so you can't get certain values in the settings.
I just had a quick look at your log files. I need to spend some more time looking at the logs; but, these two events suggest something is odd with your ignition.
At 53.3 seconds

At 133.4 seconds

The white trace on each lower graph is your base ignition advance. Engine speed and MAP are changing small amounts; but, your base ignition timing is going through rapid swings greater than 10 deg. Do you have a very sharp change in your ignition map around 900 RPM? I looked at other places on the log with similar RPMs and MAP values and I didn't see similar movement in the ignition advance (I scanned the log quickly so I could have missed things).
I don't know whether this variation in the ignition timing is what is causing your problem; but, it is something that you should check out. I also note that your TPS is reading -4% (presumably closed). I don't think that would cause your problem; but, it can create some problems with the throttle cut depending on what settings you have for throttle cut. I try to program mine to give 0 to 1% closed and around 99% fully open. There are some rounding off things that occur in MSExtra with the A to D converters so you can't get certain values in the settings.