I can't say for sure which file the information is stored in (I would have suggested
resume.dat if you hadn't excluded it already), but a quick run with Process Monitor showed a lot of promise.
edit: In response to your comment, I assume you haven't worked with Process Monitor before. So let me give a little detail about what I did.
First of all, start Process Monitor. Then start µTorrent and perform a change on the priority of a file (or whatever change you want to know more details about). Then close µTorrent.
You will now have captured thousands of events in Process Monitor.
Try to find an instance of uTorrent in the list, right-click it and select "Include uTorrent.exe". This will create a new filter, which will hide every event not generated by uTorrent.exe.
You could now proceed to hide certain actions. For example, if you right-click some "TCP Send" or "UDP Receive" events, you can select to hide those (be aware that the column under which you perform the right-click has an effect on the contents of your context menu).
Creating those filters will allow you to quickly drill down to the action you're interested in.
I, personally, was left with a few
CreateFile calls to the µTorrent related files in my roaming profile and several access actions to Internet Explorer caches (which is due to the web related functionality in µTorrent I assumed).
I would assume you have far deeper knowledge of what you're expecting to see and what you're interested in, but I'm sure Process Monitor will reveal the information you're looking for.