In 16.04, all window managers show this problem. In previous Ububtu MATE versions, only compiz had this problem: when using marco it did not occur (I would use MATE Tweak to swap when using the java app). Hence the regression issue. I am not sure if it is in MATE or in icedtea.
The java application is HOBLink JWT (http:// www.hobsoft. com/products/ connect/ jwt.jsp) which is a remote desktop client which I use for access to my office network.
In 16.04, all window managers show this problem. In previous Ububtu MATE versions, only compiz had this problem: when using marco it did not occur (I would use MATE Tweak to swap when using the java app). Hence the regression issue. I am not sure if it is in MATE or in icedtea.