Ear scratching, head shaking

I took Phoebe to the vets four weeks ago. She was doing a great deal of head shaking and ear scratching which came on quite quickly, not like a slow build up.The vet believed that it was allergies and prescribed Canaural for 5 days. She felt that attempting to discover her allergy would be like trying to find a needle in a haystack and that Phoebe would just need to be treated for flare ups when, and if they occasionally occured. The vet said she has very narrow ear canals, there was some ear wax and her ears were also very hairy, it was therefore quite difficult for her to get a good look, but she saw no evidence of ear mites. (Our pup has been suffering from ear mites and I've finally managed to get them cleared up. Obviously I'm wondering if Phoebe has caught them, however there is absolutely no brownish grainy stuff being produced and the entrance to ear canal looks perfectly clean)
We discussed SM, she checked Phoebe and there were no tender spots or discomfort in her neck, shoulder area. I did point out that many dogs always make contact when scratching with SM, as the vet's first question was - does she air scratch? I mentioned the possibility of having Phoebe MRI'd but the vet felt that this was not necessary.
I'm aware that Canaural contains Prednisolone, would this only relieve possible SM symptoms whilst she was being treated with it, or would the drops offer her some relief for some weeks after the end of the course? Knowing this would help me to determine if possible SM sumptoms have been masked for the past few weeks. Three weeks after we finished the drops, she is starting to scratch again, it's certainly nowhere near as bad as it was, but when I take her back to the vets if it continues, I don't want to go down down the route of allergies as so many have on this forum, if we are just wasting time with a misdiagnosis. It is also a possibility that we are just having problems breaking the cycle of ear mites in a multi dog household, but as I said, there is no discharge or rubbish being produced that would indicate ear mites.
Knowing the effects of the Prednisolone in her drops would help me determine how I might move forward with our vet if we need to go back. Can anyone offer me any advice please?
Sorry for the long post, but it's a bit pointless asking for advice without all the facts

I'd guess that it is more likely to be ear mites or something in the ear canal. Only 5 days with Canaural is very short. I've always done at least 7 days and for ear mites you really need two weeks of treatment as far as I understand to stop the mite life cycle. Also they could remain as eggs in bedding etc -- it really takes a major cleaning, washing, vacuuming, and usually treatment of all dogs and cats in the house at the same time.

I would think on the basis of only seeing this -- every fast onset and history of mites in the house -- that an MRI would be a pretty big step.

Prednisalone will help SM symptoms as well. But I'd try a longer course of treatment for mites, then check ear infections (the Canaural should address those if there), trim hair from ears, make sure they are very clean. If scratching persists, I'd try changing foods/look into other allergy causes. What abut fleas with a new pup? Rabbit mites?

If nothing else seems to help this then I'd consider discussing an appointment with a neurologist. But generally that head shaking usually indicates something in the ear canal.

Thanks for the reply Karlin. Both dogs are due to be Frontlined, so will get on with that tonight. I did wonder about Phoebe's diet, but I really hope we don't have to change it, as it's pretty finely tuned in order to keep her colitis under control. She's on Royal C. Cav Specific, I guess I could change to RC Allergy kibble? I think you are right, ear mites should be the first thing to be addressed so it looks like a prolonged treatment for both dogs for ear mites in order to break the cycle. I just don't understand why Phoebe hasn't got the brown flakey rubbish in her ears like pup had when I was treating her for ear mites. Is Canaural the best treatment or is there anything else you can suggest that might be more effective? Pup was prescribed Surolan, which do you think might be better?
What are rabbit mites, do they affect them all over, or is it just the ears?
We do take them to a local beauty spot regularly for walks, so I'm wondering if they may be a possibility.
Fingers crossed we can get to the bottom of this