I want to read around the subject a little so I can reverse engineer what I have done. I never plugged the ports in my old place, but did use the system for a week in my new place without plugs. I understand what is happening, I just want to know why it is happening.
What you suggest sounds about right. In my old place My speakers were on rubber feet direct on to wood. The new place is carpeted and I have spikes -> tile -> carpet. I was quite disappointed as I was expecting to notice an improvement with the reflection reduced on the floor and I was expecting bass to tighten up because of the spikes-> tiles. But nothing happened, it sounded identical (if not slightly worse) than my old place. I then tried the plugs as a last ditch thing, thinking it would only affect the bass. The only reason I tried the plugs was that the lopsided setup worried me. Was pleasantly surprised by the results. If the bass frequencys were trampling all over the modifications I had just made, that would make sense.