I'm taking a swing in the dark, but something similar happened to me. Do you have any software firewalls installed? (Let's say ConfigServer / CSF)
I recall my first server bottlenecking because of a lot of ill-intended activity on the forums. Bots, hacks, exploits, etc,. ConfigServer stopped 80% of this and Mod_Security did the rest. What's your server environment? What are you using to prevent ill intended behavior?
You're not utilizing anti-flooding. I've managed to do a small flood on your website and the server locked up for a minute. (With good intention) This is something you should consider fixing.