Similar problem with chrome x64 latest. I have a group with chrome and some chrome desktop app -chrome pages saved to the desktop- (all same user). If I open a different chrome user instance from the grouped main chrome, the window jumps out of the group after a couple of seconds. Also, the grouped chrome windows (six tabs in my case) change their order ( for example: the first one before opening a new user chrome window become the third, or fourth...the second beame the first and so on) so I need to rearrange them again. Not optimal I think 
Also, even with "Group all chrome.exe windows automátically" ON, when I open a Chrome Desktop app -chrome pages saved to the desktop-, they don´t go to the group with all the chrome.
One last note Chrome related: sometimes, when activating one of the groupy tabs with a chrome desktop app, all the group minimize on its own. Odd.
I´m using Groupy 1.11 beta (with 1.1 all these Chrome stuff also worked as I related it do with latest Groupy beta)
Thanks!