It's been a while since I saw PT LE 5.1, but any 5.1.x should be able to give you bona fide stereo tracks; that was the whole point of 5.1, at least in LE (in TDM that was the version that surround capability came out, including the 5.1 surround, get it?). I may be actually acquiring a 001 in a few days, so I can help you more then if you don't find your answer.
Question for you: When you set up your track to be stereo, do you SEE level meters for both channels (and pan sliders) in your Mix Window? If so, something's probably wrong with how you've assigned your inputs.
If you DON'T see dual level meters etc. for your "stereo" channel in the Mix Window, then you probably didn't CREATE a stereo track. When you go into the (is it File or Edit?) scroll-down menu and pick "New Track," make sure you select the right TYPE of track in the appropriate drop-down menu (I think it's called "track type" or something; it's the same drop-down that you use to create a master fader, if that jogs memories). Don't select "2" tracks, as that will get you 2 mono tracks (and they both may be defaulting to input 1, or left-channel input).
Does this help? Is is too basic? Is it just plain damn wrong because I'm going off memory? Best of luck; let us know how it goes.