Looks like no one's responded yet, so thought I'd chime in...
This is the first I've heard of this one.
I've noticed that sometimes I'll enter a match and my gun is not working properly - i.e. the upgrades I applied are not there. I have to restart the game for it to work. However, this is pretty infrequent. It's possibly a related issue, but certainly not as severe as what you are experiencing.
You might consider trying a different mouse or updating the mouse drivers. Sounds like a bit much, but, that's about all I can offer up.
I'm assuming you've already checked the mouse settings in the Options menu.