That was expected actually. Had to run a database import that took almost 11 hours, during which time we experienced server loads ranging from 5 to 10, which is fairly high, and it'd be totally normal to experience lag in that situation.
Typically on any kind of shared hosting (GoDaddy, etc) you see loads from 2 to 5. On a box like we're now on, the load should be below 1, and hopefully it will balance out in the .1 to .2 area. Any load time over 1 means the server is behind, anything under 1 means it's able to keep up. We'll see how it goes, but you should see much better performance.
Please let me know if you continue to get those issues. I've been doing a lot of mysql optimization, and have a bit more to do yet. Some of the optimization requires services to be restarted, which could result in very brief (under 1 min) downtime. In any event, if you continue to have issues, try and explain what happened as best you can, and I'll look into it further.
Load times are under .1 today, which is lightning fast. Hopefully it stays that way.