I can't believe they are not treating for both either. Candida allows the not so good bacteria to flourish. That bacteria will eat up the B12 leaving none for you.
In the meantime, if I was in your shoes, I would do the following until they get their act together:
Oral methlycolbalmine (B12, the methyl form) will help. Jarrow makes a 5000mcg methly form. This form does not need to be converted to a usable form and there's a high enough dose for gut to absorb what it needs. Take it on an empty stomach for the best results.
For the candida, eliminate all sugars (natural and artificial) and white breads,pastas and rice. Also eliminate all fermented products and mushrooms and anything with yeast in it. You pretty much go on a whole fresh food diet. Nothing processed, not wine, beer, soy sauce, mustard, etc. Add in a good probiotic to re-establish good bacteria that will keep the bad in check. Again, Jarrow makes a pretty good probiotic. I usually order many of my supplements from
www.iherb.com
This is just my two cents but if you google B12 deficiency and candida, you'll find tons of info on how to deal with both naturally. I'm sorry that you have to deal with this and that your docs are not more supportive.
Marlene