Also sometimes intervalometer stops after the first picture in Full Silent Picture mode. The only fix that I know is to remove the battery and try again
Use "leave menu" as trigger.
You need a "Picture review" time (not off) in Canon menu set up.
The camera is/might not be stopped, it just waits for your input (buttons?) since, I believe, you did not set up a review time.
What are your power saving settings? Be aware of this bug:
https://bitbucket.org/hudson/magic-lantern/issues/2265/turn-off-lcd-enabled-stops-intervalometerDo upload the (a shorter) MLV with your issue.
Does it happen when saving as DNG (instead of MLV) in camera?
Tried any other program for MLV ? ( MLVFS? MLP for Mac? MLVProducer? )