Bobby, as the other replies have indicated, plugging one of the ports affects the bass, but has nothing to do with your situation. You have the means to at least partially correct the problem, but you appear to be handcuffed by a "purist" dogma which doesn't reflect the reality that source material, rooms and speakers are imperfect, but can be improved by processing.
I never use any type of "direct" mode; I want to use the processing features that I bought my receiver for. For example, the "Audyssey" (not the "Flat")equalization curve has a gentle treble roll-off, amounting to about 4dB at 16KHz which helps on material which has excessive treble content. Applying a 3-4dB treble cut with the tone control might help if you can overcome your reluctance to use the features that are designed to help you.
