Another possibility is the MTHFR gene mutation - have you been tested for this?
According to the STTM site:
"What a defective (mutated) MTHFR gene does to you:
...
You can find yourself with high folate or high B12 i.e. your body will have problems converting inactive forms of folate and B12 to the active forms. So the inactive folate or B12 will simply build up in your serum, also inhibiting the active forms. Most serum folate tests are actually measuring folic acid, which needed to be converted to methylfolate to be used metabolically.
..."
www.stopthethyroidmadness.com/mthfr/