Welcome to MedHelp Lyme -- and good for you for thinking through whether your current doc's approach is most effective for you. Lyme disease is an area of medicine with much confusion among the medical community, and it will be a while before the docs all agree about how to diagnose and treat for Lyme.
Like all antibiotics, doxycycline ('doxy') is more effective in some illnesses than others. That's to be expected -- but in the case of Lyme, there is a serious split in the medical community. Lyme disease hasn't been recognized for more than a few decades, and the early docs assumed that a wellknown antibiotic like doxy should be good enough to treat the Lyme.
From what I have read, doxy may work well if given very early in a Lyme infection, but many of us do not know how long we have been infected: I never saw a tick or had a rash, so I don't have any idea when I was first infected. I was however quite ill with Lyme and another infection (babesiosis) which is also often carried by the 'Lyme' ticks.
As more time has gone by in the medical world, recent research has discovered that the Lyme bacteria do not respond to the usual antibiotic treatments like doxy. Why? because Lyme bacteria have a relatively long reproductive cycle compared to most other bacteria, and it is when bacteria are splitting to create more bacteria that the antibiotics can best kill off the bacteria.
The result is that doxy and similar antibiotics are not able to kill enough of the Lyme bacteria to cause a cure for the patient. Therefore your '2 full rounds of Doxy' may well not have been at work long enough to kill the Lyme bacteria thoroughly enough to end the infection.
If that is indeed the case, then it sounds like you may have not been treated long enough to kill the Lyme bacteria. I saw a bunch of MDs before finally getting a diagnosis of Lyme, and I got myself to a Lyme specialist who knew what antibiotics to use and for how long (think: 3 or 4 months, not a few weeks.)
Doxy is not the only antibiotic that works against Lyme, and it may be that there are other antibiotics that are even better. My doc did not treat me with doxy, but off the top of my head, I am not remembering the antibiotics that were used. It takes time after treatment for your body to get back to feeling normal and healthy, but it's definitely worthwhile. It's been almost ten years since I was treated for Lyme (and babesiosis), and I remain entirely clear of both infections.
Your doc sounds like s/he is following the supposedly 'standard' approach to Lyme treatment, but in your situation, I would find an ILADS-member MD for a second opinion. Best wishes to you -- let us know how it goes, okay?
PS It looks like you are near Philadelphia, yes? I just did a quick search online, and there seems to be an awareness of Lyme in that area, as well as MDs who may be quite helpful.
The medical community is split between MDs who are Lyme specialists vs MDs who only think they are Lyme specialists, but are not up to date with diagnosis and treatment. It's good news that Lyme may have a selection of Lyme docs ... if you're running into problems in finding a Lyme doc, let us know, okay?
Take care! Lyme is a misery sometimes, but it is indeed treatable and curable.