Like TSchrief stated look carefully at the hot shoe to see if that small switch is sending a signal to the camera making it think a flash is mounted.
At ISO = 3200 the basic exposure for bright sun would have been f/16 at 1/3200 sec. Even slight overcast as you mention would have yielded a stop more; perhaps 1/3200 sec at f/11. I would have thought that any of the pictures you took at ISO 3200 and where the shutter was limited to 1/250 would have been terribly blown out (over exposed).
Can you post a picture here with EXIF attached? We might be able to tell more what is going on. For one thing the EXIF will clearly indicate if a flash was attached (even if it wasn't).
By the way, you likely will not perfectly freeze the wings of a hummer solely with the capability of the 60D. To freeze all motion in a hummingbird's wings, you need a shutter speed of 1/5,000 to 1/20,000 of a second. Having said that, I think that sometimes the slower end, which the 60D can do, the lsight evident motion improves the shot.
Go to http://www.rpphoto.com/howto/hummer/humguide1.asp
for some good tips on "hummer" photography.