what seemed to disappear in the track was the pickup up note that it starts on, which both precedes and finalizes the loop. i'd notate this in 4/4 and make the loop four bars, so you'd end up with the following if you were to notate it:
x |: 1... | 1... | 1... | 1..x :|
...with the pickup note where the xes are. so, it's just an extra quarter note at the front of the pattern...
i don't know how, but something got confused somewhere, as it sounds like the pickup shifted to the one, which just put everything out of order.
like i say - this is very weird...