One of the problems with Lyme is that the spirochete that causes it is hard to see without using dark field microscopy. A recent test, requested for Lyme came back negative for syphilis. (Considering I was faithful to my wife for 23 years (up until her death) and haven't had any opportunities to catch syphilis in the time since, that was a real comfort. I was more concerned about a tick bite.)
Another is the dogmatic assumption that 'you can't have Lyme disease, because it isn't present around here' (despite having been bitten by a tick 2000 miles away).
Until the medical establishment gets its head out of its ass, it will continue to be a problem.