Hi and Welcome to the forum! You have asked some very good questions and gotten some great answers. I'm going to give my answers, even though it will repeat some of what you have said.
1) First, when the first MRI was done, it was likely just the regular work up one gets for the inital look see for headaches. It behooves any doc to be sure first that headaches do not reflect something more serious. That MRI should the 12 lesions. Yes, migraines can and do cause lesions. But the lesions of migraines do not have serious neurological symptoms accompanying them. Headaches, yes; neurologic symptoms, no - not unless they have actually been having mini-stokes.
So, the radiologist would have had access to your sex, age and whatever info the ordering doctor had put on the requisition. It is usually brief and probably said "Migraines". The radiologist saw the 12 lesions. If these lesions were mostly subcortical, then they would have been "consistent with" migraine disease, but the radiologist was being thorough when he remarked that the lesions might also represent a demyelinating process like MS. The neurologist knows that you didn't have more neurologic symptoms and accepted this - rightly so.
So in the intervening couple years, you started having other stuff that we all might write off as age - actually inappropriate unless you are pushing 70 - but we do it anyway. The vertigo (common in people), flashes of light (actually not a factor in garden variety bad eyesight) and weakness of your hand (are you under 80? - should be happenin'). So a new MRI shows the same lesions. But, now we have a whole new framework to evaluate both MRIs in. The new neurologist was not constrained by the history of only migraines. Perhaps we can fault the first rad for being swayed toward migrain as the likely cause of the lesions, but it sounds like he opened the door to consider MS.
In 2007 you had what was very likely a type of early MS situation called Radiographically Isolated Syndrome. This is where the MRI is showing the lesions of MS, but the patient has no symptoms. Most docs will say that you can't diagnose MS without the symptoms. We understand this ONLY in retrospect, though, now that you have had symptoms totally consistent with MS.
The radiologists had different "indications" for doing the imaging. Hindsight is 20/20.
2) In making a diagnosis the neurologist must account for everything they know. In this case, he now has to account for new onset of demyelinating-type symptoms. If these lesions had been caused by a one-time event - the symptoms would have occurred at the time of the event and would have been present since then. This did not occur. We know that many, many people's MS has been discovered by doing an MRI for other reasons like working up headaches or head trauma. The lesions are found and there is nothing to associate them with. The symptoms are usually not that far behind.
We had a member here who was an MRI tech. Her hospital got a brand new, super keen MRI machine and she was allowed practice on it. She persuaded her fiance to be a guinea pig and ran one on him. He had a brainful of lesions - no real symptoms. Within weeks he began having full-fledged problems. Weird, but true.
We have a current member who started with the Radiologically Isolated Syndrome, began having a few minor symptoms and is now diagnosed and having doubts about how it all came about. But, this is one of the known ways MS can present.
3) I would say that is is common to have an increase in symptoms and no increase in lesions to account for them. There is an often a remarkable disconnect between symptoms and lesions. There are often symptoms for which no lesions can be found and vice versa. There are lesions, but the person does not have a specific symptom that seems to be caused by that lesion. We have a Health Page that talks about this:
http://www.medhelp.org/health_pages/Multiple-Sclerosis/Lesions-vs-Symptoms/show/61?cid=36
We often get angry with the dunderheaded neurologists that try to match up the two things and then try to say that MS is or isn't active depending on the results. MS is NOT that predictable.
4) Yes, many of us have been diagnosed with a MRI that has not yet shown changes. I am one. My MRI showed only a single spot on my brain which was deemed normal for my advanced age of 53. Two years later - and a few more symptoms - it was the same. My MS Specialist felt it was all he needed for a 90%+ confidence that I had MS - well enough to begin treatment. To be thorough, thugh, he sent me to a better machine for a better look at my spine. I had six lesions that had not shown up on the prior lower resolution scan.
The good neuro, and it sounds like you have one, does not worhip the MRI as if it is "All Revealing". They know that it is just one of the tools they use in making the diagnosis.
BTW - your physical exam showed damage to the CNS in two different spots. The hyperactive reflexes show unequivocably that you have a lesion in your spinal cord. The nystagmus indicates that you likely have another in your brainstem. That combines with your history of weakness in the hand (a third location) and some cognitive stuff.
It is probably inevitable (an oxymoron? lol) that you will have more lesions develop. Maybe not. A certain number of people go through their entire life with exceptionally mild symptoms and few lesions. Most have a rougher course than than and show progression in the disease and the number of lesions.
If you are into some long (not so heavy, but long) reading. I tried to explain the McDonald Criteria in detail. These are one of the paradigms used to diagnose MS. You fulfill them if you have had at least two different bouts of symptoms. You have at least two sites in your exam that show signs that the central nervous system ahs been damaged in two or more areas and you have lesions that are "consistent with" MS.
I assume your neuro has sent the many blood tests that look for signs pointing to the many mimics of MS. This is mandatory before the Dx of MS can be given.
Here is the Health Page that describes how the McDonald Criteria are used. As you near the bottom of it you will see a list of "scenarios". You need go no further than "Scenario I".
http://www.medhelp.org/health_pages/Multiple-Sclerosis/Diagnosing-MS---The-McDonald-Criteria-revised-2005/show/370?cid=36
I hope this, along with everybody else's comments, helpful.
Quix - Founder and President of the support group for people who talk too much
ON-AND-ON ANON