I used to own Magnepan 3.6rs and I feel there is nothing wrong with your speaker system. Magnepan's frequently "bottom out" or make a slapping sound when playing heavy bass notes with rock and roll or other music at moderatly high levels. This phenomem is also frequency dependent. Most people just live around this problem because the speakers sound so good and refrain from pushing them. Some find it frustrating because first they play so clean it is easy to play them very loudly and not realize how loud they are playing, then you are suddenly rudely reminded by the "slap" sound. Second it is important to use high power, high current amps with a high damping factor to control the panels. The more power the better and some solid state fans use Bryston 7b monoblocks with success. Others like the softer sound of tubes with the high frequencies. A good combo is a tube preamp and solid state amps for the 3.6rs.
Some people advocate using subwoofers in conjunction with the pans but the slapping sound can still occur at high levels unless you use an electronic crossover or a home theater processor to filter out the low bass notes. A problem with this method is trying to find a subwoofer that will blend well with the Maggies which might be getting easier as this technology improves. I would look into the Vandersteen subs or the new Velodyne digital or the Revel B-15s.
I don't know why you'd contact Martin Logan about Maggies maybe you typed in the wrong words in the second paragraph. I'm sure they would tell you to sell the Maggies and keep the Martins.
I have always preferred the Magnepan sound over the Martin Logan sound by a wide margin, because to me, Martin Logan has never successfully integrated their woofer system with their electrostatic panels well.
Magnepan for marketing reasons denies that their speakers need a subwoofer, but they could sell a bunch of dedicated sub panels with the 3.6rs and other models if they developed a system that could incorporate the Tympani bass panels with a special crossover for the audiophile who wants to take this to the limit.
Or, hmm, since Magnepan put Apogee out of business and I believe won the rights to the Apogee technology in the patent lawsuit, why don't they use the Apogee ribbon technology and incorporate this into their speaker systems? I've never heard anyone complain about Apogee bass as long as you had the amps to drive them.
And yes, if your Maggies are in need of repair, they would have to be serviced or adjusted (sometimes the panels can become out of line) by Magnepan.
Also if you are getting "bass slap" beware! You are endangering the ribbon tweeters which seem to blow easily despite being fused. They are user replacable and if not under warranty, I believe sell for around $200-300. They are a pain to replace though.
All previous cautions to the wind, the 3.6r is a wonderful sounding speaker, that do have some limits (The BASS), but what they do well (the mids and high frequencies) is close to are is "state of the art".
If you are a dedicated rock and roll man this may not be the speaker for you.
Hope this info helps,
Steven