The only thing i can come up with is Soft Rot.
This usualy starts at the neck of the onion wich is usualy the softest part and works its way down. Normaly the first sign small yellow blotches which turn brown and the onion rots, this normaly happensduring storage.
An onion will normaly drink about an inch of water a week, thats why you dont water them to often so combined with all that rain we had and also the soil not being able to dain it away the onion the onion has taken to much moisture.