This could be any number of things and without being able to inspect everything it’s hard to tell what it might be.
In ISA 2006 their is a setting that ties 1 user or session connection to 1 IP (or something to that effect) which generally speaking means that only one user at a time can request a webpage/connection. This can cause a monumental slowdown of services.
Double check that this option is not locked down in this way. I’m sorry i can’t be more specific however its been a long time since i’ve delt with 2006. I’m sure someone else on here can give some more details.