I have the same with the vu-meters and the window size, and another one I've noticed is that when loading a file, it gets added to recent items, but if closing and reopening the program, the item has been disappeared. But when doing this for the second time, it seems to remain there
All of these appeared in .40
I think this is also related to the bug which I reported. I noticed the same problem myself. This is what I noticed. When you first run the program, it creates an INI file in the windows folder which has the same name as the executable. This file stores the toolbar, screen resolution and recent file settings. So this is the INI file which it reads the recent file list from unless you rename the executable. If you rename it, a new INI file is then created based on the new file name and it then reads the recent file list from the newly created INI, making it appear as if items have disappeared. For example, when I first downloaded the package, the file was name mptrack_Generic-1.17.02.40.exe. I renamed it to just mptrack.exe. I found two INI files in the windows folder, mptrack.ini and mptrack_Generic-1.17.02.40.ini. However, I believe that even taking this into account there still seems to be a probably related secondary bug because I'm still getting inconsistent results on the recent file list. I.E. Items disappearing and reappearing from the menu on subsequent runs of the program like Relabsoluness described.
Personally, I think that when you work out all the bugs, having MPT create the INI file based on the name of the executable is probably a good idea, but it should still be created in the same folder as MPT, not the windows folder. This way you could have multiple copies/different versions running in the same directory with their own individual settings.