Hi becky723, welcome to the board!
Regarding Lyme disease, it is possible you were not treated long enough and/or aggressively enough initially. It is also possible you were bitten again. Many people are bitten without knowing it. What dose of Doxy did you take and how long did you take it? What dose of Amoxicillin did you take? What side effects did you have? Are you still being treated?
Lyme symptoms do wax and wane. Lyme can cause lesions on the brain. Which Lyme test did you have done? You have a positive test and symptoms, I think you should be treated.
Below is a Lyme symptom list. You can have any combination of symptoms.
It is very important to see a knowledgeble doctor. Many doctors do not understand Lyme and treat with outdated protocols. Besides Lyme, ticks can also transmit several co-infections including Babesiosis, two types of Ehrlichiosis (HME & HGE), Bartonella, and Mycoplasma. Many people who have Lyme are co-infected. It may affect treatment choice and progress. It is important to be tested for these by a Lyme reputable lab such as IgeneX in Palo Alto, CA. Have you ever been tested for these?
If you need a doctor recommendation, you can email me at email@example.com
Are you aware of the Jarisch-Herxheimer Reaction (herx)? Often when people who have Lyme take antibiotics, their symptoms become worse or they get new ones. When the antibiotics kill the bacteria, toxins are released making them feel worse. It can be very scary, but it is a good sign the antibiotics are working. Although it can vary individually, many people experience this at the beginning of treatment and every three to four weeks. I wonder if this is what you experienced?
It is also important to learn as much as possible. I recommend reading Dr. Joseph Burrascano's 2005 Diagnostic Hints and Treatment Guidelines For Lyme and Other Tick Borne Illnesses at http://www.ilads.org/burrascano_0905.html He is one of the top Lyme doctors in the country, and many Lyme doctors follow his protocols. I also recommend the books "Everything You Need To Know about Lyme Disease Second Edition" by Karen Vanderhoof-Forschner and "The Lyme Disease Solution" by Kenneth B. Singleton MD.