Congratulations on the success of your forum. Like Auge, I looked at your site and it looks great! I love the aesthetics; I think you nailed 'clean and simple'.

I'm not going to pretend I understand the database structure and optimizations there, but on a basic administrative level - is your hosting optimized for the kind of traffic you get? Msql and Apache (if Apache) are rarely ever set up on VPS for 'real' traffic. Also VPS vary tremendously in quality and configuration etc. What is causing the issue? The database size? Parsing tables? Memory usage? CPU? Honestly, compared to most standard php/mysql forum applications MLF is pretty low fi and very tweakable.

My own forum runs on an embedded device using only non-volatile memory card/s for storage. It has practically no traffic (and never will) but I'm curious to know what sort of resource issues you are running in to in the long term.