Preferences not carried over since 9.0

I upgraded from 9.0 and no preferences were carried over it seems (no custom workspaces, custom vst plugin lists etc. etc.). I had not customized my profile name or anything (was named Default-2 I think), the one created in 9.5 was named Default-3.

I went in the appdata directory and copied over the 9.0 files over the 9.5 and things seem to work again in terms of customizations, on the other hand I’ve noticed for example that MediaBrowserLocations.pxml has become MediaBrowserFavorites.pxml with a name change inside also, and am concerned other files I copied over might not be correct.

Is there anything else I should be doing? For example one of my workspaces had mixer on the left monitor, main window center and mediabay right, but no matter what I do mediabay does not open on its own when I create an empty project, I have to open it manually and then it does show on the correct screen.

During installation I had several complaints on 9.5 that it lost the USB connection to the dongle and I should put it somewhere else, and the same happened when I launched it the first time, so I moved the dongle from a hub to directly attached to the PC and that hasn’t happened since, could that have caused issues with the preferences migration? Note that 9.0 never gave me the dongle error message even after installing 9.5.