Hello,
Sorry to hear you are having issues.
For the first one. Please try to set so that application to auto group when open new instances. Right click on apps groupy tab to open the tab menu. Refer screenshot below.

As for Acrobat, yes there are some application not working properly with Groupy. I have forward your report on Acrobat to Stardock Support Team for their assistance. Please keep an eye on this thread for any updates. We appreciate your feedback and patience.
Thanks
Basj,
Stardock Community Assistant.