Default MTP problems (folders show as files, contents never update, etc)

Hello all. I had been having some problems using MTP with my Moto X (I always have had problems with MTP on any device tbh). First off, I was noticing that file and folders made on my Moto X never seemed to show up on my PC when connected via MTP. I tried to remedy this issue and force an update (as per this thread). I used the SD scanning app found here. Apparently I shouldn't have done this with my Moto X, because now all folders in MTP show up as files, and are not able to be opened anymore. I've tried reconnecting my phone, and I've tried enabling/disabling MTP. About to try a full reboot. (EDIT: full reboot didn't fix)

Did I just derp this install of my phone? Great... back to square one.

How do I get the stupid files to update automatically with MTP. It absolutely frustrates me that it doesn't seem to know when a folder has been added.. I understand the differences between mass storage and MTP, but wtf... I should be able to at least access files and folders 2 days old.

Edit 2: Which Windows services does MTP use?
"Most people, I think, don't even know what a rootkit is, so why should they care about it?"
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