It is difficult to say for sure simply because it is the one that gets almost all the traffic.
What I have noticed is that another script will slow down when things get flaky so I have to guess that all scripts are affected. I put timers into a test script and what happens is the thing hangs for a few seconds and then fires off full speed with no delays during execution. If I run a php script that outputs the phpinfo() it does the same thing at startup and then takes a few seconds to display all the information. This happens when I'm on the machine itself so it's not a network issue but appears to be related to a bandwidth issue.
The error is related to the app pool so my guess is that maybe there is a setting I need to find to increase requests or bandwidth to the app pool? I still can't find anything on this anywhere :-/