I do love mate, but nearly every 2nd time I boot the panel (for me on the bottom windows style flickers, shows no icons and is unusable. When I re-boot, a dialog says “Panel not responding”.
What I do then is to reboot and chose an older, generic kernel in Grub. In 9 out of 10 times this heals the problem and I can reboot successfully afterwards. I have the Mate panel 1.14.0 and the desktop environment 1.14.1 installed on Ubuntu 16.04.1 LTS, upater ran this morning.
Just curious as to which compositor you are using. I’m running UM 16.0.4.1, Mate 1.14.1, kernel 4.4.0-34-generic with nvidia proprietary drivers installed. I don’t use a bottom panel. If I ran Compiz boot and shut down times increased considerably and the top panel would flicker off then on after boot or reboot.
In the past I have had issues using Compiz. So I decided to start there in the elimination process. I changed to Compton and flicker problem was solved, boot and shut down times were better, but still on the slow side. At this point I purged Compiz and boot and shut down times sped up considerably. The best I can figure even after switching to Compton there was some part of Compiz still running in the background.
I don’t know if any of this will help. Just relaying the issues I had.
Sorry I didn’t get back sooner to check on the status. I’ve been tied up at work. Glad to see that v3xx pointed you in the right direction and things seem to be working now.