Check if "Report combined pedals" in the Logitech Profiler is checked. If it is uncheck it. In the options menu of LFS go to controls, make sure the throttle/brake axis are seperate. You should also see buttons 1, buttons 2, etc until you see Axis, click on that tab. If you push your brake/gas/clutch you should see axis bars on the right moving. Click on the control you want to assign to which axis, then click on the axis.
Good luck.
EDIT: You can also invert the axis if necessary, eg. the thottle / brake are at full even though you aren't pressing them.