I was thinking that the tortoise looked a little puffy, and being that your vet is concerned with this after actually examining it, I would be concerned as well. I cannot see anything with the eye in the pictures, but if it's getting better, then good.

It might be a good idea to run some blood samples and verify that everything inside your tortoise is running A-okay. I'm sure your vet has at least mentioned this.
A vitamin A deficiency? While they symptoms "may" indicate this, it would not be a final diagnoses unless adequate diagnositics were done. Treatment with vitamin A supplementation has no negative effects, and thus was probably given to cover bases.

Once you have settled in with a vet that is easy to work with, and seems knowledgeable and resourcefull with reptiles (it is impossible to know it all!), I would stick with him/her as moving from vet to vet reduces a DVM's ability to help your animals.

Ian

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