My ds2 was on placed on the SEN Register half way through reception year, because he was significantly behind the other children in his year. He is nt (sorry neurotypical, so has no special needs as far as we are aware) and just needed extra help to get him through. Initally they thought he had slipped back due to a prolonged period of illness (nearly died from encapsulted pneumonia in December 2008) but personally I feel he wasn't achieving long before he fell ill.
Via the SEN register and his IEP he had additional, targetted support in the areas he was struggling, both in class, in little groups and occasionally 1-1.
He is now just about to go into year 2 and has just been taken off the register as he is now achieving at a much higher standard. In fact his teachers and the SENCO said that he has come on so much in the past six months that he is way ahead of all the groups he is in and will be moved up to the next group on entry to year 2. He is only now at age 6 1/2 starting to find his feet academically, but once he got going he has gone from strength to strength. I'm sure your ds will find his way as well.
I suppose my point is that some children just aren't as academic as others and some sometimes need additional support to help bring them on. Its by no means an indication that they will always struggle, just that they need more help at this particular moment in time. Its good that the school has recognised this and are giving him the extra support he currently needs.
I do understand how you are feeling though, as until ds2 went on the SEN Register I had never even heard of it and was quite upset at first. I felt I must have done something wrong, as his brother is extremely academically able and we had stupidly assumed that ds2 would follow suit. I too wondered how it was that they had both been brought up the same yet ended up so differently abled iyswim. I know your two are twins and that would make it seem more like they should be evenly matched, but I'm sure they too have their own strengths/ weaknesses, likes and dislikes etc. I guess to a certain extent, even twins are individuals.
I now realise that my boys have very different personalities and likes and dislikes etc so it naturally follows that each child is an individual whose strengths and weaknesses will also be individual. Ds1 is very academic, brilliant with facts, computers etc and ds2 is very creative, loves music, art and drama etc. They both have strengths, just in different areas.
I know its difficult to accept at first, but being on the SEN Register isn't a bad thing, its good. It means he is getting the help he needs to achieve his potential.
If however, you feel in your heart/gut that there is something more to his struggles, you can either go to your GP to discuss your concerns and ask for referral to a Developmental Paediatrician or ask the school to have him assessed by an Educational Psychologist.
If you are thinking dyslexia, but he has been tested and they say its not that, have you considered the possiblity of dypraxia? Lots of people think of dyspraxia as just being bad a sport and not able to ride a bike etc, but there's far more to it than that. Some of the indicators are very similar to dyslexia and the two things can sometimes go together which can make it difficult to separate them out iyswim The Dyspraxia Foundation Website is a good place to find out more.
hth