On Windows 8.1 Update 1 the taskbar button is the responsibility of the OS not ModernMix and it may be the OS is unable to correctly handle the scenario you would like.
What I have done is get an added registry key for the next build which should revert the taskbar buttons back to being under ModernMix control. Note that you will have to disable the OS option for showing taskbar buttons AND you will not be able to use the OS provided close button in fullscreen apps or apps will not close.
It will be able to be enabled by adding the key ModernMixDoTask as a string with a value of 1 to HKEY_CURRENT_USER\Software\Stardock\ModernMix\mmix.ini\ModernMix
Be aware that this will require v1.15 AND we will not offer any form of technical support for that setting. If it works great, if it doesn't then sorry.