We're more used to many words spelled "contra...", based on the Latin for "against". There are very few words spelled "Contro..." where it's a variant and with the same meaning. I guess the reason for the "a" pronunciation is just through our being more familiar with "contra..."
Think it depends which part of the country you come from - taking accents into account. Stewey - being a Scot I would put the emphasis on the "tro" in controversy.