Mine both have bowel problems.
They are also gluten intolerant - so much so that they get gf food on prescription.
Their bowel problems did lessen significantly when they went gf, but they haven't disappeared totally.
I have had a long running fight with their paed who insists that it's behavioural. In my youngest, yes, I agree. He's mostly fine, but if he's busy, he won't realise he needs to go until it's hanging out of his arse. Then he'll pluck it out and carry it to the loo 
but my eldest still soils and he feels so bad about it. There's no way he's choosing to do it. He suffers from awful bloating and bouts of constipation followed by diarrhea (my spell check appears to be american, sorry about that!) which may be seepage round a big block of poo!
We used to use lactalose, which was fairly good but the effects didn't last long, but just got the gp to prescribe something called laxido, so we'll see how we go with that.
I have heard of so many people with children with asd who also report bowel problems that I feel it can't be coincidence.