JonnaBunn
This is partially caused by auto playing module, But if you put Play and Stop button and Goto Layout2 Button in layout 1 this can be solved.
if button play clicked then protracker stop, after then click go to layout2, when back to layout 1 click play to continue playing.
Consider layout1 event sheet like Load module scene and never jump there again. Place event on layout2 and 3 ; use play and stop on those layouts.
However i must adjust some functions on original source... i will ask J.Halme permission to change the code.
Please test this .capx
http://gigatron3k.free.fr/html5/C2/plugin/ptrck.capx
Regards