Would be good to get thyroid looked at again as treatment with B12 can affect the levels of thyroid medication that you need - so if you have medication then the levels may need adjusting.
Another possibility is that your body is reacting to the additional B12 in your blood by trying to shut down the transport of B12 to the cells causing functional B12 deficiency. Unfortunately if you are in the UK I don't think you can actually get any tests done to investigate that ... and GP would probably laugh you out of the surgery if you asked ... but you may have a good GP who wouldn't.
There isn't much in the literature on treating functional B12 deficiency but what little there is seems to imply that they only thing that works for some people is keeping the levels so high that your body can't make enough antibodies to stop it all getting through to the cell level, so may be that you need a lot more B12 than you are getting.
Some people report feeling better if they get lower doses of B12 ... and that could be another way of dealing with functional deficiency - stopping the levels getting so high that the auto-immune response kicks in - but things vary so much from person to person and there hasn't been any research that I'm aware of so that is all pure speculation on my part. However, the individuals concerned were experiencing giddiness at the times of the maintenance shots which doesn't quite sound like what you are descibing.
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