Usually a high C-reactive protein level shows imflammation in the body.....usually due to another autoimmune disorder, or something else. It is not normally indicative of your thyroid issues. It just compounds and adds to your thyroid problem. :(
You need to have your Dr. dig deep and find out what is going on.
My C-reactive protein was high last year also. My pcp asked if I'd had any infections or anything going on at the time of the test -- I didn't -- but he never acknowledged that I even HAVE Hashi's and he was not interested in looking further for any other problems - he's not my pcp any more either........I was having a lot of thyroid inflammation at that time, but I also have pernicious anemia and some arthritis, so it's hard to say why the C-RP was high -- actually, about that time, or shortly after, I found out that I have a leaky heart valve (recently found out, it's the aortic valve), so I don't know if that could contribute or not.........
I have mitral valve prolapse which sounds like the same thing you mentioned, this was diagnosed on accident because I started having heart palpitations. The rheumatologist suggested that I follow up for more testing once my thyroid gets back to normal. A lot of these ailments seem to go together. Have you been tested for Lupus?