This has driven me beyond nuts over the past year and I've had no luck hunting down a solution.
Basically, I use a Logitech G5 mouse because I like being able to program the various buttons to things like Back and moving windows between monitors.
The problem I have is whenever I open up certain programs, the pointer speed settings change to a much faster level and even interfere with button settings. I can get the settings back by opening Setpoint and clicking OK, but it's a real pain.
Currently, the offending program is Perforce on 64-bit Windows 7. In the past, I ran into the problem with MySQL Workbench on 32-bit Windows XP. So two different computers, OSs and programs. Same issue. It's not a long list of programs, but in both cases, it's a program that I use a lot. If I change the mouse settings after opening the program, it messes up the settings once Setpoint is reinitialized. So I have just needed to suck up the faster mouse speed setting while Perforce is open.
I have the latest version of SetPoint and mouse driver, at least the last time I checked a few months ago. I've been dealing with this since 2011.
FYI - I'm using SetPoint 6.32.7, driver version 5.33.14.