It's quite common for Candida to produce a die off (herx) very similar to Lyme: www.thecandidadiet.com/candida-die-off.htm
The best way to deal with it is just as one would deal with a Lyme herx - detox, detox, detox! www.thecandidadiet.com/candida-die-off.htm
This could also be combined with herxing from starting the flagyl as well. so detoxing becomes even more necessary. If you can't get the herxing under control soon, then it's always advised to reduce the dosages of your meds for a short time to help control the herxing, then slowly (while still keeping the herxing under control) raising your doses back up to therapeutic levels again.