Yes, something like that. Most likely it was due to some thin low clouds passing in front of Jupiter but it could have also been due to wind making the air unstable causing more refraction. Also, towards the end of the time-lapse it was mostly due to the altitude, the lower Jupiter was in the sky, the more atmosphere light had to pass through resulting in a blurred image.

This is also why telescopes are usually on mountain tops, to avoid the effects of atmospheric distortion as much as possible :)