In the scoring software that I use (Noteworthy Composer), each channel (that is, each part) has its own stereo pan control, used to adjust the left-right balance. A similar control ought to exist in other products.

If you look up "pan", "stereo", or possibly "balance" in your documentation or help file, you should be able to see how to set your different channels or instruments to all have the same pan. That will get rid of the stereo difference, so the good ear accurately hears the volumes you've assigned to each channel.