I think the VPS is a poor choice for anything but a static site. I had the same issue with phpBB so I moved to a dedicated server.
You've got some 20-30 users with an unknown amount of sites hosted on the VPS. The sites are doing their thing, and on top of that you'll have staggered backups and cPanel and WHM upgrades going on. Check to see the server status through the NetStatus Monitor and you'll notice that if one VPS is in the red or hogging resources it will drag down all other sites with it.