Clarifying edit:
This is of course when I use the admin pages. (regular FTP work through FileZilla works pretty fine) As I understand it, Wordpress is downloading files to the server through FTP when I do these operations. When this is finished, Wordpress should refresh into a new page that says that everything is complete. It doesn’t. The WP installation is correct, and no plugins can possibly cause this error. Hence, I believe this is some sort of a server config issue.
I have this issue on all my installs on this server. I’ve had it on another server as well, but never put any work down to solve it that time. I’ve also had it working on other servers with the same Wordpress install.