I can't speak to your specific case, but I am not faster on around town rides with gears vs. my fixed gear so I'm not shocked by your results.

Having said that you'd need to ride the geared version of your bike a bunch of times to see if there was any external factor on that specific ride that caused you to be slower. I had a 25km bike commute with 1 traffic light and a variation of 10%-20% in avg speed was easy with different wind conditions and depending how I felt that day even though the bike was exactly the same.