Does the medication say that it does treat pop eye? Sorry, I'm terrible with knowing if a disease is a fungus or not.
I also don't use medications often, but stay strict to the instructions on the medications.
If it allows you to, do water changes as often as you can. IMO, whenever a betta looks sick,the first way to go is: Water changes daily, and appropriate amount of aquarium salt.
Sorry if this didn't help too much.