So, the baxtr "drag and drop and drag again" workaround was marginally successful for me, but didn't seem like a scalable solution, so I did some more digging. I discovered Shane Monroe's invaluable "A Practical Guide to Installing and Configuring SubSonic" here:
http://monroeworld.com/android/subsonic/ (which I can't believe I hadn't read before).
I'd already set up my rig (Win7) correctly according to this guide, EXCEPT for the "Permissions to remote folders" step about a third of the way in. I ran through that part to grant Subsonic Log On As A Service rights, then restarted my machine. Lo and behold, all of the folders that had previously been missing are now present and accounted for (as I suspected, there were many that I forgot I even had).
I didn't have time to add a new folder after having changed these settings, to see if this solves my problem going forward, and I'm still not sure why some folders showed up and some didn't in the first place, but I'll update this thread with my results when I do so.
One question for the board, though - Shane mentions that
many people will "condemn" the use of the administrator account for this purpose because it violates "good security practices". Once you have SubSonic actually WORKING, then you can go back and make designated user accounts and implement all those "good practices".
I'm not totally clear on what kind of designated user accounts he's talking about here (accounts in SS? Accounts in Windows?), or precisely what the security ramifications of this setup are. Can anyone enlighten me as to best practices from this point, or if they agree that this current setup is suboptimal from a security standpoint?