From: http://www.pigeonrescue.co.uk/illnessesandinjuries.htm
Trichomoniasis commonly known as canker
Canker is caused by a flagellate protozoan. It is not transmitable to humans or other mammals but can be caught by other birds that share the same water, eat seed dropped by an afflicted pigeon...
It sounds like it could be canker. Treatment for canker is Metronidazole, which is Flagyl and can be purchased for fish and pigeon without a prescription. Can you post a picture of it?