It's most likely due to server load. I've been watching Lotus's CPU usage via cPanel today and the load is anywhere from 11.86-60.57 in terms of Linux Loads which is always a sign of heavy load. It's Lotus being slow. The issue is most likely from some loose ends being tied up from the recent server work.
As for the MySQL, do what gsonline stated above and check over your configuration files. MySQL should be working despite Lotus being loaded at the moment since my website has been working fine. It has SMF 2.0 RC2 and the most recent build of Wordpress on it.