Okay, so I was using the trial, which may have been an issue. I added the RPA license to my account, and PAD popped up and said the license has been added, and now it is behaving differently.
I was able to complete the connection using my domain\username login, and it doesn't complain when using the Connections tab.
However, when I go to set up my flow, it now allows me again to select the desktop flow from my environment/machine, but it gives the same errors:

When I choose attended mode, that error disappears, but when I try to save the scenario, it is blocked with this message:

I can go back under "Connections" and update it again, and it seems to be successful, but I get the same errors in my flow again. I will also note that the second error is now appearing for other flows where it makes no sense:

This popped up once for a different flow that has existed for months, and even though I verified the Dropbox account it was asking about (that never changed), now it shows up every time I go to edit that flow. However, it doesn't block me from saving the flow in that case, and it works normally otherwise.