There may be nothing wrong. Just because you can't manipulate the input levels independently does not mean they or your computer/sound card are not functioning properly.
The point of channel inputs is to just make sure that the data (music) stays in its designated channel and not, I'm assuming in your case, to equalize them as they are captured. That is really the function of the editing software.
Pull in some data and listen to it in your editing software. If it sounds like it does on the original, then all is well. I actually don't recommend that you fiddle too much with varying the input levels which is really a re-engineering of the sound as one captures audio. Bring it in at the highest possible undistorted gain and, if necessary, boost one channel in the "edit" room.
I'm not sure anything is wrong.
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