The mouse acceleration is a big bother for me as well. People experiencing it and also looking in this thread have probably already done this, but just in case:
1. In the Control Panel>Mouse>Pointer options menu make sure to un-check "Enhance Pointer Precision"
2. If you have a Logitech mouse and are using the Setpoint software, be sure that you have "Mouse Acceleration" set to "None" there also. I believe that it's set to "Low" by default.
In regard to the problem itself, it is not a framerate issue. It is present at both high and low framerates, but is exacerbated by lower ones. I am not talking about mouse LAG here, but the mouse acceleration.
Just my two cents.