So I played around with the domain for a while, but nope. That didn't make a difference. Obviously not, that’s just for file sharing. The DNS setting in QNAP was set correctly, so it couldn't have been the DNS, right? Well after a few hours of frustration and database reinitializing, I googled harder.
And got this: http://stackoverflow.com/questions/1292856/why-connect-to-mysql-is-so-slow. The MySQL DNS doesn't bother with the settings in QNAP. So all I had to do was change the MySQL configuration my.cnf file on the QNAP file system. Which I had no idea how to access.
Luckily there was another Google result that helped: http://forum.qnap.com/viewtopic.php?p=124900
So I downloaded PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html), SSH'ed into the NAS, navigated to /etc/config and then ran VI on my.cnf. Of course, it'd been a decade + since I used VI and it's interesting key combinations. A university had it all written out for me (http://www.washington.edu/computing/unix/vi.html). I picked an abritrary line at the start of the my.cnf file, added
skip-name-resolvesaved it, restarted the server and hey presto! Connections were almost instantaneous again.