Just so you know I did a quick check just to make sure as I have been awake all night doing electronics here and forgot if I checked it before or not!.
Ok I loaded up the new version of BPM, I then went to the "user" tab at the far right of the icons above the libs list, "the folder".
I then browsed to my "loops" folder where some of my test loops and performances are. I right clicked the folder and then the "add to favourites" bar shows move your mouse over this so it highlights yellow and click to save. Then I closed BPM completely down, I even turned the computer off and then back on after a few mins, started bpm, checked the favourites list and my loops folder was still in the list right where I left it. I then selected remove from favourites right click the folder in the title bar when opened move mouse over to highlight and click to remove and it was gone. so you can now add and remove.
heres a few pics to show you
so yes the favourites issue is fixed.