Not sure I can help but from some of what I read online, the AMA is used as a diagnostic indicator of PBC. One Dr. wrote that there is about 2% of patients who have a positive reading and do not have PBC. Why did they say they were not diagnosing you with PBC if your results were positive, have you asked? Are your other LFT's (liver function tests: bilirubin, Alk Phos) elevated as well as your ALT/AST? Did you see a hepatologist or were the tests ordered by your regular doctor? If you haven't seen a hepatologist yet, then you should ask for a refferal. They may schedule a liver biopsy to confirm and check for what type of damage you have, if any or at least try to figure out why your ALT/AST are elevated (how high were they). Are you scheduled to have a follow up blood test?
Are they looking any deeper as to why you are anemic, have low total protein and have blood and protein in your urine or was it a trace amount?
Again, double check with your doctor and if you aren't comfortable with what they say, ask for a refferal to a specialist.
Diagnosed with AIH January 2007,
CMV (cytomegalovirus) June 2008
Raynaud's February 2010
meds: Azathioprine 100mg, Ursodiol 250mg BID