Well the title explains it all, using the latest beta and Media Player Classic HomeCinema, if you enable the always on top titlebar button, then click off of MPC, the next time you click back on it disables the always on top effect, denoted by the button backlight turning off.

So, you enable the button so it glows, click off of MPC, click back onto it, and the button stops glowing and the AOT function is disabled as well. You can then click the button again and repeat the entire process ad infinitum

Also, going into fullscreen has the same effect, but I bet its the same issue regardless. The button can also disappear when coming back form a fullscreen state, however I can not consistently reproduce this.