Oxford explicitly states they expect A-levels to be taken over the typical two year period with 3 exams done in year 13. I suspect however if you have extenuating circumstances explained by your academic referee this will be considered. Cambridge is less explicit on this but does also note that any extenuating circumstances should be explained in the reference.
I expect this would be similar for other medical schools - generally they expect them to be done over 2 years, doing the same subjects over 3 years is a potential issue (the exam boards being different is not a factor), but depending on the extenuating circumstances this may or may not mitigate it.
Make sure your academic referee explains the situation in your reference basically, and I'd probably suggest contacting the medical schools to enquire about how they consider A-levels done over 3 years where there are extenuating circumstances.