Thanks for sending the config!
I loaded it into a test machine and changing folders is completely instant, so it must be a combination of the config and the machine/environment.
My bet is that something is pointing to a device or network drive which is very slow or inaccessible.
Something thing to try, along those lines, is clearing the recent list and favorites:
For the Recent list, right-click the path field and choose Clear History.
For Favorites, go to Preferences / Favorites and Recent / Favorites List and right-click the root node for an option to clear the whole list.
Of course, make sure you still have your config backup, or make a new one, so you can restore the list afterwards.
Those are the only things that stand out to me.
(There's also the folder-change script, but it's disabled and so shouldn't do anything. And the other script should only do anything when a new window opens, so that can be ignored.)
If clearing the favorites list is what fixes things, it's probably going to be an entry in the list that's pointing to something that is no longer (or not always) there, and which takes Windows a long time to give up looking for. (Inaccessible network drives can do that.)
It could also be tied to the Jump List settings, which are configured to add all the favorites to the jump list. I'm not sure if jump list would be reevaluated on every folder change (at least with the other settings in play) but it could be involved. But maybe you already tried turning all of that off. (Windows will only show a maximum of about 10 items on the jump list anyway, although it doesn't provide a way for us to know when we add items.)
If you still see the problem, it might be worth creating a Process Monitor log of what happens when changing folders. That should reveal what is being accessed, assuming it is triggering some kind of filesystem activity. It may also reveal which part of Opus, or potentially a 3rd party shell extension, is causing the access/delay.