Hmm, when you installed the Logitech software did you complete the calibration? If I recall correctly you will be required to press all the pedals and you'll see an indication of pedal travel; did that bit work correctly?
You might be able to check those under the Game Controls in Control Panel (might be differnt in Win7).
Since you said it works great, I assume that all other pedals are working fine? i.e. brake pedal just as it is supposed to?
In the Controls > Axes/FF menu, when you press the throttle pedal the the corresponding "yellow bar" move as expected?
[From LFS Manual]