Hi Yar...The antibiotics you mention I am familiar with, but I have not really heard of too many instances of them being used on small lizards. I am no expert in this, I just to use these two antibiotics regulary at work. What form are you offering to your lizards, and at what concentration (powder/liquid)? A more common antibiotic is Baytril, and is used commonly in reptiles.
It's been a while since I've read up on it, but I think the Flagyl is used primarily for flatworms. Have you had a fecal done on your lizards. At the least, any vet should be able to give you an indication if this is internal worms or protozoans infecting your lizard. It may be worth invetigating, as there are several people that I trust here that could tell you what types of meds and doses to treat your animals with. First get your confirmation from your vet.
Being so small, the lizards are very succesptible to renal failure when overmedicated, and can be succomb to a slow death. Give plenty of water when you are medicating and also keep them warm. That usually means putting them in a controlled temp enclosure where they will never drop below 85...even at night.
That is my only thoughts on this right now.
John E.