Welcome, Alec.
My first question: Have you updated your drivers?
The drivers on the install disc are most likely outdated. The original drivers for the EIE were not good, but the updated versions are fine in Windows.
When you click on the ASIO Pannel in Preferences>Audio>Driver Settings, you can see the driver version.
I am using 2.9.55.
Your Mac friends may be out of luck until Akai updates the drivers for the latest Mac OS. I have seen some complaints about that.
Assuming your drivers are current, what is your latency set to? If it's too low, you can get pops.
Which version do you have, the EIE (red face, 16 bit), or the EIEPro(silver face, 24 bit)?
I have some other ideas, but answer these questions first.