I'm going to try updating the MS software (there is a newer version available). I'm running SetPoint version 3.1.116 which is not the newest version of SetPoint but was the last version to work without issues (the newer/newest versions are very buggy).
The Intellipoint settings that won't stick are related to the "pointer options" tab (i.e., pointer speed, enhanced pointer precision, etc.).
I haven't found any other posts or information on this issue. Thanks for your help.