Roy,
Without going into alot of details here are a few general suggestions.
If you are running some P2P apps, it will cause serious lag issues.
If you are hosting a vent server on your box same.
Disk I/O is often the culprit for what you are describing, most would point to the network, but something tells me you are ok with your network connection, unless you are doing some p2p, then the amount of connections your using to do that would greatly impact your connection to mxo.
Hit me up if you want to talk specifics.