Strangely, I have exactly the same problem on my MacPro but not on my MacBookPro. I changed the sidebar on both computers to contain my favourites but after closing all the windows on the MacPro or restarting, the sidebar returns to its defaults.
hmmmm... I am also having the problem with a MacPro 5,1 mid-2012 10.12.16
I was also experiencing some full blank screens as I tried to create new browsers from saved settings. So I de-registered and used AppDelete to get rid of any "extra pieces" or legacy files in case they were creating the problem. Then I reinstalled PF8 but unfortunately I experienced the same issues.
At this point I have downgraded to PF7 (7.6.2), seems to be a couple too many issues with this version and I need to get my work done. PF7 works fine for me and the features are good. I also find the sidebar in PF7 to be easier to use than PF8.. not sure why though. And it remembers the favorites which happens to be the primary feature that I do use.
In addition, on my MacPro PathFinder regularly freezes when I try to close a window (spinning ball of death) and I have to force quit it. Never had this before. I might have to go back to v. 7 just as you did.
Yep this fundamental bug is affecting me too. In PF7 the sidebar favourites always reflected Finder, which I found useful. At the very least, my changes were never lost. I'm struggling to see anything in PF8 that I find useful over and above what PF7 did, and PF7 worked with no problems!
In another thread Jordan has admitted that this is expected behaviour -
"Please make sure to save Sidebar preferences in its preferences window (gear button next to the Sidebar title). Creating new file browser uses default PathFinder preferences.
This behavior is often questioned by PathFinder users so our developers will review it when they get a chance."
I find this incredible given the number of times he's come across like they don't know anything about it - I really don't thnk I can trust Cocoatech any more...