Ben - You say it's not the speakers because you've 'swapped them over'. If this means that you physically moved the speakers each to the other side and the problem remained on the left, then you are correct. But if this means that you only swapped the speaker connections left for right at the amplifier end, and the problem remained on the left side, then the left speaker could still be your culprit (likely a fault in the LF driver, its crossover, or its connections).
But if you did in fact rule out the speakers (and speaker cables, tested separately) by physically swapping them side for side, then the CD player, its interconnects, or its assigned amp inputs would be suspect, since you imply that your other sources do not show the same problem, and these possibilities could be tested for by likewise performing separate channel swaps or gear substitutions for each.
But there is another remote possibility: the player's output could simply be just a bit too "hot" for the amp's input stage to handle cleanly on certain LF peaks, and these may be channel-specific in the program material. The only reason I characterize this possibility as unlikely is not because it doesn't ever happen (I've experienced it myself, though it affected both channels equally), but rather because your player and amp are both made by the same manufacturer, and should not exhibit this degree of incompatability.