As i see, this looks like a problem when your computer input is being blocked: other programs continue working, you can connect to your computer by network, kill war2 process and computer will work fine after that.
I don't think this is a virus-related problem, i also don't think some reg-cleaner or chkdisk thing will help. Of course try that if you can.
I think looks like this is hardware or driver problem.
Maybe a videodriver, maybe some kind of controller. As i remember, some similar problem caused with old war2insight versions with different CPU cores. Maybe you should try to force process affinity to CPU0, try it.
Also you can try CPU savior: http://forum.war2.ru/index.php/topic,409.0.html
Maybe the problem is too high CPU load in some situations.
Can anyone call this problem or get it in every game? This looks like a big problem, but the main problem that we can't call it when we want for debug purposes. Maybe we can add some kind of watchdog into loader to check if war2 hangs up and to kill the process or even debug it...
What we can try is to collect statistics: OS version (xp,7,8), CPU (Intel/AMD), video card (ATI/Nvidia and version), video driver.
I'll try to add this information collecting into my next loader version...