It sounds like youre recording a mono signal through your computer soundcard's line in and recording to a stereo track in Audition. Because the line in is a stereo jack, it is routing the mono signal to the left channel. This is normal. But what's complicating matters for you is that you are recording to a stereo track as well, so it's recording that signal to the left channel as well.
What you need to do to fix this is in Audition to click on the "Rec 1" button for the track you're recording to, and then in the dialog box that pops up, select the "Left Channel" option instead of the "Stereo" option. This will then record the mono signal coming in on the left channel of your soundcard as a single mono track. Then when playing that track back, you can pan it however you want.
G.