I recently installed Java version 8 on my Mac. Since then I have found two problems with sub-windows: if you have more than one sub-window open at a time and activate one of them, the others disappear until you de-select the active window and activate the main game window. The other problem, which is more serious, is that you can no longer move counters between sub-windows and the main game map. This is a problem for games where the sub-windows represent cards in the boardgame that are used to hold pieces temporarily. I have found that Alt + mouse click will let you move pieces from the map into the sub-window, but the same combination will not let you move them back out again.
I didn't find the right solution from the Internet.