I've been experiencing a ton of lag ever sense I switched to MySQL database instead of flatfile. Any ideas on what is causing this?
I'm actually not sure on that. I use MCProHosting, and they allow you to create databases. P.S. I am running your latest version of UltimateTickets, could that affect? http://www.spigotmc.org/go/timings?url=16562334
Based on the timings, I would say you're running an off-site MySQL database. I'm not sure how MCProHosting handles MySQL databases, but if it's possible to get a locally hosted MySQL databases, that would greatly increase performance. If your MySQL host is 127.0.0.1 or localhost, then it's locally hosted. You may want to verify this. Also you stated that PEX uses an incredible amount of RAM, that doesn't seem to be the case. According to your screenshot you are only using 670 / 1979 MB, so plenty left. You probably referred to the percentage of the tick it occupies.