Could be the result of internal bacterial infection. I would treat with Seachem Kanaplex (Kanamycin sulfate) and see if you see any changes. This medication is okay to mix with methylene blue.
If you are adding water conditioner with every water change, you need to wait at least 3 hours after adding the water conditioner before redosing methylene blue for the total tank volume. Water conditioner will make the methylene blue inactive when it is added to the tank, hence the 3 hour wait time.