There could be a number of reasons:
1. After reading the book "Cure Unknown," apparently there are a large number of Lyme strains, not just one. So you could have one that isn't very reactive to the ABX you've taken thus far.
2. Everyone immune system is different and because of this, we react differently to different ABX.
3. Potential coinfections
4. Possible misdiagnosis...not something any of us like to think about, but a possible reason nonetheless.
I have a herx affect almost immediately when I take abx. According to Dr. Burrascano, one should see a herx within 48-72 hours. This is the time it takes abx to reach full circulation in the body.
This is just my thoughts off the top of my head, but I'm sure other more experienced members will be along shortly to give you some good answers to your questions.