One more update, still no fix. It's still there, it's just not working. Problem related to new Dock perhaps?
Code:
silver:~ strings /Applications/Parallels\ Desktop.app/Contents/MacOS/Parallels\ Service.app/Contents/MacOS/prl_disp_service | grep IconGroupingEnabled
IconGroupingEnabled
IconGroupingEnabled.patch_stamp
.IconGroupingEnabled
Warning in class 'CVmSharedApplications': tag 'IconGroupingEnabled' is absent
signalIconGroupingEnabledChanged(bool,QString)
signalIconGroupingEnabledChanged(bool)
slotChangeIconGroupingEnabled(bool)