As you may or may not know, after the MvM update came out, the particle table started having overflowing issues.
In order to fix this, you need have the latest particles_manifest.txt located in your /tf/particles/ directory. If you don't have this simply update your server or grab it from your games GCF file.
For the systems you don't want loaded on your server, simply remove the exclamation mark thats located in front of the system name. You can refer to my signature link for a list of what's loaded in each system.
For your convenience I've attached a version that doesn't load the majority of MvM particles. Simply place this in /tf/particles/.