Does port location make a significant difference with regard to speaker placement?

Ports are a poor man's way of avoiding bigger speakers.
They will always dish out unwanted artifacts, it is unavoidable.
They used to be just one solution, now they are almost universal in box speakers..
Subwoofers invariably utilise ports.

If you don't like it then go panel like I did and accept you won't have full-on bass for the last 30Hz.

“Also try a sock-puppet in the port”

Ah!...much like Tekton in that regard

Front ports or a lower plinth port are less fussy. Rear ports should usually be placed with a good amount of space between it and the rear wall. I'd say at least one foot from wall. Some manufactures using rear ports sometimes recommend close to rear wall for bass reinforcement.

Thanks everyone for the feedback.  Let me answer some of the questions posed here:  
@erik_squires yes I'm going to try the foam port plugs and should have sooner.  The reason I didn't is I had a friend of a friend who really knew his stuff come by my old house years ago and Sumiko the *&^% out of my system.  The results were awesome but he definitely frowned on the plugs.  
@noromance Loudness is a guilty pleasure, I recognize it would contribute to the phenomena in question and I do turn it off if needed.  Gear and a pic are listed in my virtual system, figured most would click it to see.  

Also, big picture I did stop by one dealer yesterday and listen to a few things I thought would be of interest.  Suffice it to say I was underwhelmed and I'm back to optimizing what i have, which is very good, but as we all know could be a bit better!  

Based on the picture in your profile, that's a good looking system! The distance of your speakers from the wall looks pretty good too. 

A handful of things (you probably know many of these):
1. Is the base still muddy when you turn off the sub? If no, and assuming you don't have a high pass filter on your mains, the sub may be the culprit.
2. Is the base still muddy when you stick a sock in the speaker ports? Many speakers/subs come with foam inserts to tailor the sound of the bass region. 
3. What feet are you using on the Monitor Audio Silver 6 and the sub? I placed Herbies Threaded Gliders under my speakers and some Hudson Hi-Fi feet under my sub, and those made a giant difference in cleaning up my muddy bass. Speaker/sub isolation is essential for me.
4. To hit the price point of ~$1000, the Monitor Audio Silver 6 make some compromises. The bass region may be one of those compromises, so an upgrade may be in order since you're looking for that next level up in quality.