Yeah, it's very odd.
I do use the cmd line upgrade - there was one in particular I was trying to download and zip to put on our web server now.
It is allowing me to get to the server cmd so perhaps I will just try and upgrade and see what happens. I'll probably open a support ticket if it's still failing.
Thanks for your time!
Quick update if you are curious (or if anyone else comes across this at some point) - upgrading resulted in the same error. I copied the 2.6 folder and placed it in a new parent directory and was able to log on just fine with all apps working normally.