Hi Tanya:
Don't worry until you know you have something to worry about. :flwr: I spent a lot of time worried one of mine had SM and he turned out to be clear -- but has PSOM and perhaps some hind brain compression (CM) causing some mild scratching. The dog I assumed was his fully clear half brother is my most-affected dog with SM.
There are many things to eliminate first -- it is just sad if others kept passing him along without proper care. It may well be something like allergies to something in the house or outside that bother him only when awake and running around. Dogs with SM often scratch in the night (this is often an initial tip-off) or right upon waking up. But there are so many variations for the causes of scratching and discomfort that all you can do is start working through the possibilities and try to keep him comfortable til you get an answer.
If every cavalier on this board had an MRI scan probably a third to half would come back with a syrinx, going by incidence in research groups and what breeders have been told by neurologists like Geoff Skerritt, who scan breeders' dogs at low cost in the UK for their breeding programmes. While there is a debate over incidence, the fact that several breeders, some prominent in the national club in the UK, have confirmed that Mr Skerritt is seeing about 50% affectedness of all the random dogs breeders bring in suggests this is probably a conservative figure (as the condition is progressive, and breeders would mostly scan younger dogs, not the over 5's they are no longer breeding from). You will get a lot of denial about the percentages but those percentages are being stated by breeders who would initially have been far more sceptical.
However all indications are that many dogs with syrinxes never are symptomatic and many more are very mild. While this is no excuse for leaving this horrific situation as it is in the breed or accepting it as a 'norm', as some truly idiotic people have suggested we should do (not least as every sign is that the problem is getting progressively more severe and it seems there are few completely clear dogs to breed from), it does indicate that many people will never realise their dog has SM, and many more can be made very comfortable on medications or via surgery. I have had my worst-affected dog on a moderate level of medications and he is now 6. He was diagnosed at 1. Most people would never notice he has a problem; the meds manage the discomfort quite well for him. We just take things a day at a time.
The good thing is that you care so deeply, and are on the right path to get him diagnosed with whatever the issue is, and have already helped make him more comfortable.
We will all hope it is something easily dealt with.