Matt - I would try some salt baths and see if they help. Mix 2 teaspoons of salt in 2 liters of your tank water and soak your axolotl for 10 min. Time the soak as salt can damage skin and gills.
Salt baths can be given twice a day.
Before using any medication made for fish read the list at the bottom of this page http://www.axolotl.org/health.htm
for a list of safe medications. Avoid anything with malachite green as it is toxic.
Furan-2 and Nitrofura-G have been recommended for skin problems.
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