Oh, there are lots of different ways to go about performance tuning mysql. I'd start at
mysql homepage. I've signed up for the newsletter and find it very informative even tho we don't currently use mysql at work.
One difference is the whole gui environment itself. I like using them (actually, I'm bad about doing lots of stuff in a gui that I should really just stick to a command line) but they can use an awful lot of system resources so the first thing I'd try is starting the system in a command line only mode (init 4? I forget which one to use
) In this case you can always run the server without a gui running and still use a client for the mysql server on a different system.
The other thing I'd suspect when using virtualbox is what type of disk image is used as a dynamically expanding disc can cause lots more io overhead when the disc needs to grow. Maybe try moving to a fixed size disc and see if that helps.
I'm no expert obviously but I hope I at least pointed you in the right direction.