This issue came up in another post and I experience it as well.  Other people do not seem to have the issue.  It seems to be specific to certain WB themes - you probably see it with some themes and not others.  I did send support a ticket to be sure they see the issue.  You may want to send them one as well, and tell them what graphics you're using:

https://esupport.stardock.com/index.php?/Tickets/Submit

Personally I'm wondering if it's compliments of a MS-updated driver.  I'm using Intel HD4600, what are you using?

Those 2 themes work fine for me, so I guess your issue is "similar but slightly different".  I'd go ahead and start a support ticket, in the meantime perhaps someone will come along here with an idea.

One thing you can do if you like is create per application exclusions in WB for the configuration programs so WB doesn't try to skin them, that should get rid of the pause for those programs.  Not a great solution, but an option.