I can't get into certain parts of Junktown or the Hub in my game; for example, I'm trying to get to the shops in the Hub but after I walk down the main road to a certain point I can't scroll down any more to get into Downtown. Am I doing something wrong? Or is my game FUBAR?

Here is working fine. Try reinstall, maybe was some error in the installation.

I had this too in a few occasions, both in Fallout 1 and 2.
With me it happens when I scroll to any direction too quickly which causes my character to be off the screen.
It fixes itself within a few seconds or when the character comes back on the screen.

When you say you can't scroll any further, are you in the "entrance" part of the hub, needing to get to "downtown"?
If yes, then you need to look for a green shading near the bottom of the map, at the end of the road, when you step on that it takes you to the adjacent section.
if no, are you stuck in "entrance" without being able to get to the end of the road, or are you stuck in "downtown" not able to view the rest of the map?

like this

It turns out I had the resolution wrong on a mod I installed. So I fixed that, thanks for the help!