I second what sleepwoken had to say -
Some antibiotics kill bacteria during their cell reproduction. The Lyme bacteria has a life cycle of about a month, so some people herx every 3 - 4 weeks, as their cell membranes split open and toxins spill out.
Herx's can make a person feel worse than before they started taking medicine. New symptoms can also appear during a herx.
Sleepwoken was right - the best thing to do is flush those toxins right out with a lot of water, healthy eating, detox baths, and other detox methods.
I'm going through a herx right now. I can tell because about once a month, I feel even more crappy than usual and my rashes come back.
The good news is that I know my medicine is working - Yay!
Acidopholus is a great thing to take also. The best quality pro-biotics (as they are called) need to be kept in the fridge. Try not to take them 2 hours before/after your medicines or they will cancel each other out.
I take Doxy. I've been taking 600mg per day for 10 months straight. It's helped me. But the thing that has helped me the most was treating my co-infection. Were you tested for co-infections?
Please stay out of the sun. I was careful and I still managed to get burned. Its not like a normal sunburn - more like a chemical burn and it lasted for weeks even though I was wearing a good sunscreen.
Aslo, within 2 hrs before/after the Doxy, avoid dairy and some minerals - magnesium I think? Anyway, your info sheet from the pharmacy should have the precuations on it. Just take 'em seriously, Ok?
I hope we didn't throw too much at you at once. LOL Lots of info!!
Is your doctor an LLMD (Lyme Literate Medical Doctor)?
Hang in there. Peace and health to you.