Yes, you are correct. I was double clicking the effect in the effect bin, changing the duration, and then dragging the effect to the time line. Applying the effect and then double clicking it from the timeline does allow changes to stick; Thanks!
The transition that I can't always center is the cross dissolve. It seems to be a problem if there is a short 4 second clip to the left of center. Perhaps there is a minimum time for the starting clip of a cross dissolve? The effect is just 1 second, though.