One thing you can do is swap the speakers over. Why swap them rather than just the cables? Because room boundaries can affect a speaker enough to make one seem quieter than the other. This is what the balance control is really for - if you have a room where the left side is appreciably different to the right side - e.g. the left speaker is close to the corner and the right speaker is in free space - then you can perceive a significant difference in level with the balance set in the middle. The correct way to deal with this is to play a mono signal through the system and redress the balance so it comes from the centre between the two speakers.
If you swap the speakers over and the same speaker still sounds louder, then it's not room interference and it's one of the speakers. If the speakers are biwirable (i.e. 2 sets of connections on the back) and you are single-wiring, check that all four terminals are screwed tightly - your treble unit may not be making a connection on the less clear, duller one.
If there is no way the room difference is accounting for the problem, then the other cause could be an imbalance in the electronics, as mentioned earlier. You can check this by swapping over left and right interconnects between source and amp (mono signal again). If there's no change it's not the CD player. Swap over the speaker cables and if there's a change it's the amp. If there's no change it's the speaker again...
If you have mismatched loudspeakers placed in three positions over the front and at the same height placed off the floor about mid height of the room with equal spacing between them, then yes they will sound tonally different.
Equalization is the only way to solve this and for that you'll going to need separate amplification an RTA and a SPL db metre, it takes hours if not days to get done right.