That same problem exists in Chrome browser as well , but I refuse to go back to Internet Explorer. I'm hoping that perhaps some day they may find a remedy for it. -- Ace --
From the sounds of it you are using an older WB build as that's not a problem with Chrome that I am aware of. You may need to uninstall, reboot and reinstall WB.
Regarding firefox, we have an update for that hopefully having QA testing next week.
The issue is WindowBlinds for Windows 8.1, not Chrome. Even with applying a custom Chrome, it doesn't always fix the issue. If one continues to experience problems with Chrome or Firefox, they need to add chrome.exe and/or firefox.exe to the exclusion list within WindowBlinds settings.
Customizing the position of the titlebar buttons will cause issues in Windows 8.1. It may show fine in explorer.exe, but there will exist issues within other window's titlebar buttons. Thre reason for this is a poor WB integration with Windows 8.1's ability to adjust the font size for the Titlebar, which needs to be set at 14, otherwise clipping will occur. (The same poor integration causes some custom WB skin colors to revert back to stock Windows colors upon waking from sleep or hibernate, as well as causing font sizes to increase with each reapply of the WB skin. For example, setting all 5 custom font options to size 8 and the titlebar to 14, upon a reapply of the same skin, all the fonts set to 8 in CP - Display will increase in size with every subsequent WB skin apply. This results in having to manually set the font sizes back to where they should be after every apply/reapply.)