Hi, seelie. Well, since I'm up and at it, I'll take a stab at this one.
A person's body does a lot of regeneration and recovery processes during sleep. In order to do that effectively, your body regulates internal body temperature (thermoregulation) differently during sleep than it does while awake.
Since MS tends to affect the body's reaction to external AND internal temperature changes and/or temperature extremes due to neuronal dysfunction, etc., my opinion would simply be that the messages your brain is sending out regarding thermoregulation during its regeneration and recovery during sleep is being interrupted or "misinterpreted" by the nervous system.
I'd say it simply comes from the normal process and difference in thermoregulation during sleep that is resulting in night sweats. That hypothesis would probably also go along with your doctor's statement about it not being MS causing it. As a DIRECT cause, no, it probably isn't. But it MAY be indirectly affecting the normal process of thermoregulation during sleep.
If it was a DIRECT autonomic dysfunction or damage to that part of the brain or brainstem, my understanding from what little I can put together, is you'd exhibit more symptoms (and probably additional and more
severe temperature regulation dysfunctions) at any time of the day, not just during sleep periods.
So..........unfortunately, although it's a big nuisance (trust me, I know what you mean, but since I'm a woman, I didn't want to make a direct comparison), there may not be a whole lot that can be done about it.
I'd still check with a physician to see what types of suggestions they can come up with to help with the symptom. I "think" the problem with trying to ask a doctor for a "diagnosis" of WHY this is happening, is where and why you'll get such vague responses from them. They simply don't have enough information about what causes night sweats in general to be able to say anything specific one way or another.
But, if you ask for suggestions from your doctor or even from the thisisms audience here on what they may have found that helps TREAT the problem, you may get some pretty good suggestions.
(I'd be interested myself!

) I tend to turn on and off the ceiling fan and kick on and off the blankets all night long.

So that's not much advice, huh?
Deb