Well, I'm not going to second-guess your vet. I would follow that regimen and let him do a follow-up and see what happens. On the skink I'm sure he was talking about ciliates (protozoans). Flagyl is the usual treatment for that, but Panacur has been shown to be effective against some forms of protozoans, especially Entamoeba invadens. Panacur is the drug of choice for most nematodes, except Rhabdias and Entomelas lung worms. A dose of .5cc orally would be about right for a snake that weighs between 1 and 2 lbs. Dosing is normally 50 to 100 mg/kg, 1 lb is about 1/2 kilo, the strength of the drug is 100mg/ml or 100 mg per cc, so that's a dose of 50mg for a 1/2 kilo snake which is at the top end of the dosing spectrum at 100 mg/kg.
Snakes have relatively slow metabolic rates as compared to mammals, plus the eggs and larvae inside the animal take a few days to mature so I normally allow a week between doses to allow for the drug to be completely eliminated from the animal before giving the second dose. That way I avoid accumulating the drug to the point of overdose, plus it allows the drug time to work in the intestinal tract. I normally do fecal floats on my animals in between treatments if possible (assuming they eliminate in that time) to see if the numbers of parasites (eggs) are being reduced. Panacur works to interrupt the reproduction of parasites as well as kill the adults, but doesn't necessarily kill the larvae or non-embryonated eggs (or cysts). That time between doses also allows for the embryonated eggs and the larvae to mature so the next dose will kill them. I have found (for me, anyway) that this method reduces the risk of re-infection due to larvae that weren't killed in the initial dose maturing and reproducing.
Speaking of reinfection, when you have an infected animal, hygeine is of critical importance. When you are dealing with parasites that have a direct life cycle such as hookworms, pinworms, lungworms, strongyloids, and protozoans the snake will just keep reinfecting himself if his cage is not cleaned and disinfected thoroughly and frequently. Feces must be removed immediately and water bowls should be disinfected every other day or so. Water should be changed daily because it is a perfect culture medium in a snake's cage. To disinfect, use a 10% solution of chlorine bleach and water. Allow it to remain on the surface for at leat 10 minutes, before rinsing and drying, then allow the cage and fixtures to completely dry before returning the animal to the cage. You can use a preparation such as Roccal-D or Nolvasan also if it's available (your vet may be able to provide you with some). Those preparations are very concentrated (they dilute at 2 oz per gallon of water) and also very toxic, so care should be exercised when using them, but they smell much better than bleach.