I think I've isolated a bug that's specific to WordPress installs on cpanel servers.
Before a domain name is mapped to a cpanel based server it's possible to access a website by going to http://myip/~myaccount/
In this scenario it seems that WP Minify does not like the "~" in the url. (I'm guessing it's that).
The error appears when I minify either js or css as a 400 bad gateway:
When I call that url directly I get a "HTTP/1.0 400 Bad Request" in the browser (black text on a white bg).
When I then map a domain to that account the problem goes away so it shouldn't hurt anyone on a production server but I did spend 3-4 hours today trying to fix it with permissions changes, adding new base urls via the plugin config screen and modifying .htaccess files.
I guess some people could also have legitimate use for the "~" symbol in their urls too so it might be good to look into a fix for this.
Fantastic plugin by the way!