It's been talked about a lot on these pages; a few people (myself included) have experienced this. No idea what's causing it though. One thing I've noticed is that there doesn't seem to be any one solution that works for everyone; different tweaks work for different people it seems.
I would advise trying either DOSBox SVN-Daum or SVN-ECE. In other words, a DOSBox build other than the 0.74 that GOG provide. I'm using SVN-Daum and it works great!
This thread might help:
https://www.gog.com/forum/jazz_jackrabbit/jazz_jackrabbit_vsync I followed this post in particular:
https://www.gog.com/forum/jazz_jackrabbit/jazz_jackrabbit_vsync/post5. I used the settings suggested by him/her but changed some to the following:
fullresolution=1400x900
aspect=false
cycles=10000
cycleup=100
cycledown=200
I changed the resolution so that it does not look stretched/squashed. There'll be slight borders to the sides if you're using a 16:9 ratio monitor like myself, mind.
Also, make sure Vsync isn't forced on in your graphics card settings.