Border is a few pixels off when grouping Visual Studio

Interesting.  We will investigate further as to why that window is behaving differently to others.

Thanks for letting us know.

Having just had a quick look, the issue isn't what it first appears to be.

The windows are aligned, it is just Groupy has mis-detected the colour of the window edges to be a translucent dark line when it does not have focus (the default OS look in fact).  This makes things appear out of alignment when shown on a dark background.  If you put something white under it you should see the line.