It has been quite a while, but I am moving forward on debugging this issue. I am currently running 4.1-2647 with download station pkg 3.2-2922 and saw the priority change for the first time in a while, plus other strangeness. With the introduction of Video Station, I was reshuffling all the files in my video share into subdirectories for Movies and TV shows. I then realized I had ~60 email downloads that I needed to change the directory the files will download into. I proceeded to highlight numerous files that shared the same destination directory, and used the edit function to make this change to them. I then did this for the remaining groups of download files.
After completing all the changes I stepped through all the files looking at their directories & priorities, and things looked good. As nothing was downloading I decided I should restart the service in case this was needed to have the directory to take place. Using the pkg service I stopped and restarted the download services. I then went back and re-entered the download station and proceeded to cursor down through each file. I found quite a few entries had reverted their directories back to the previous destination, and some entries also had changed to low priority. So the low priority issue was back and I went back file by file and changed the priority back to auto. The new issue with the directory reverting to an old entry even though it had shown the correct directory before the service was shut down, caused me to go through file by file and again change the directories to my desired new locations.
I think I can now attribute both issues to the selecting of multiple files and changing the directories or priorities enmass. Even though it appeared to take effect, the restarting of the service somehow reverted or caused the issues.
Hope this helps if anyone else is experiencing the above issues (or debugging them).