I feel really dumb for not noticing the cause sooner, I most attribute it to the rareness of the problem and the inconsistency at which it occurred.

I use a virtual server environment for my servers, and one of my measures to improve reliability and performance was to have two instances of the webserver behind a load balancer. In laymen's terms, whenever you're connecting you're assigned to whichever has the least connections and they're otherwise identical (same files, connect to the same database, etc).

Well... turns out when I duplicated the server initially, the software decided to not change the MAC address. Laymen's: The ip address of the server is different, but the network uses the mac address to map ip addresses to boxes, if two boxes have the same mac address then traffic is going to sporadically and randomly switch between them... but also with a bad IP address which means half of the traffic is always getting rejected.

So your connection to the load balancer was fine, but it was struggling to connect to the webservers and the webservers were struggling to connect to the database.

Once I changed that the server immediately became quite zippy!

My sincere apologies for the impact.