Same issue in Ubuntu MATE 15.04 with mate-menu (mintMenu fork) at the bottom panel. Same workaround - disable Place Windows plugin to get rid of the issue.
Unfortunately, the suggested fix for Whisker Menu didn't work for mate-menu. It even made things worse: now in 2/3 cases it's elevated as before, and in the rest 1/3 cases it's shown stickied to the upper left corner of the screen. O_o
Same issue in Ubuntu MATE 15.04 with mate-menu (mintMenu fork) at the bottom panel. Same workaround - disable Place Windows plugin to get rid of the issue.
Unfortunately, the suggested fix for Whisker Menu didn't work for mate-menu. It even made things worse: now in 2/3 cases it's elevated as before, and in the rest 1/3 cases it's shown stickied to the upper left corner of the screen. O_o