I am currently on Ubuntu Mate 15.10 with the ‘dev’ PPA for 16.04 packages. This is something I just recently noticed.
I have saved a panel layout with “custom layout” and I noticed that in Mate Tweak when I go from Compiz back to Marco the panels do not come back. I am on the layout (forgot the name… with Plank at the buttom) and after I go from Marco to Compiz the panel is fine but when I go from Compiz TO MARCO, the only thing on my screen are open apps and/or plank.
I did notice when I switch from custom panel layout to one of Ubuntu Mate’s default layouts (name wise) the panel is back and a-ok when switching back to Marco
-Xmetal