I know this thread is a bit old, but it's still relevant! I would like to offer an additional solution in case the simple disabiling of MATE's compositing doesn't work.
I had this same issue start yesterday after I enabled compositing on my MATE desktop. However, after I attempted to disable compositing, the issue persisted. I had to open the Configuration Editor and manually edit the Marco configuration to fix it.
Here's what I did for those that can't get this fixed:
1. Make sure the
Use compositing box is unchecked in Preferences > Desktop Settings > Windows before continuing.

- Desktop Settings screenshot
- Screenshot-Desktop Settings.png (34.34 KiB) Viewed 456 times
2. Open Terminal and type
mateconf-editor then press Enter. This opens up the Configuration Editor.
3. Navigate to apps > marco > general.
4. Make sure the
compositing_manager box is unchecked in the right pane then exit out of the editor.

- Configuration Editor screenshot
- Screenshot-Configuration Editor - general.png (93.61 KiB) Viewed 456 times
5. Press CTRL+ALT+BACKSPACE to log out. This also restarts the X window system. Log back in and this issue should be fixed.
You may have to repeat steps 2-5 if the "Use compositing" box was checked before attempting this fix. I'm not sure why but the compositing_manager box was still checked and I had to repeat those steps to take care of it. This was why I was having the shadowy, invisible menu issue. Annoying bug. Eventually it'll be patched. Best of luck!