Bumping as it's been a few days and I'm still clueless.

I solved my own problem.

I finally was able to get server-status running, straced the PID, found out that it was throwing a 425 Bad IP connecting error, and went into my FTP server (vsftpd) to add a pasv_promiscuous=YES to the file. Started vsftpd up and it worked.

That was fun.

Glad you finally figured it out! So it was an FTP config problem and not WordPress at all, if I am understanding your solution.

Glad you at least had fun! ;)

It was a big pain in the ass but I like solving things. LOL

Yeah, so the way it works is that an update goes through FTP and then to WordPress. Now, strangely the files were copying via FTP, I assume, to the WordPress tmp folder, apparently, but not copying over to the final destination (plugins directory). It's still strange and I think WordPress would do right by its users to actually communicate the errors that result in files not being copied, but I'm just happy it finally works. I doubt anyone will be able to strace the right PID to replicate. It was hard finding the right one!