Same thing here, the game doesn't detect my Micrsoft X5 mouse (under Windows 7 x64 SP0 with latest "windows update" intellimouse drivers), didn't try a PS/2 mouse yet but it can be worth trying if its a kind of "game not aware of USB" problem ...

In the interest of giving people a few more options for stuttering mouse issues:

1) Do not set vertical sync to "force off" for your video card - this was causing the stuttering for me.

2) A Windows 7 mouse fix: http://donewmouseaccel.blogspot.com/2010/03/markc-windows-7-mouse-acceleration-fix.html (I don't know if this will work or not for Shogo. If it doesn't, just re-apply the WindowsDefault.reg that is provided).

for me the only fix is open autoexec.cfg find "MaxFps" "0" if its not there add it exactly change 0 to 60 and thats it no need to use vsync or triple buffer. it also fix abnormal speed ups

Have we solved this issue yet? My mouse is one of the ones that totally does not work. I can't even use it on the Menu screen. Anything?

Bit late to reply but it seems you have to manually add the Mouse commands to the autoexec.cfg file in your shogo directory. Changing them in the game menu doesn't work. Combined with the info in this post:
http://www.gog.com/en/forum/shogo_mobile_armor_division/use_your_mouse_wheel_for_changing_weapons
I managed to get my mouse working in Win7/64 by adding the following to the end of autoexec.cfg:

enabledevice "##mouse"
rangebind "##mouse" "Button 0" 0.000000 0.000000 "Fire"
rangebind "##mouse" "Button 1" 0.000000 0.000000 "DoubleJump"
rangebind "##mouse" "Y-axis" 0.000000 0.000000 "Axis2"
scale "##mouse" "Y-axis" 0.002375
rangebind "##mouse" "X-axis" 0.000000 0.000000 "Axis1"
scale "##mouse" "X-axis" 0.002375
rangebind "##mouse" "Wheel" -10000.000000 -0.100000 "PrevWeapon" 0.100000 10000.000000 "NextWeapon"

I tried to get my middle button (Button 2) to work but this kept messing things up. Anyway the mouse works for me now.