I found that a small bug in the Oct 18 build where the opacity for an object was incorrect.
I had two object sharing the same gradient. One object was more opaque than the other even though the opacity for both was 100.
I checked the XML editor and found that whilst both objects had Opacity:1, one of them had fill-opacity:0.71.
I don't know how to reproduce this. It only happened once in an entire drawing.
On a side note, I had been getting very confused when making a stop on a gradient transparent. I would change the Alpha value and the gradient would reflect the change, but later I would see the alpha value would be 255 instead of what I had set and what I saw on the graduent. It took me ages to spot that the alpha value was being replaced with the Master Opacity. Is this something that is still being worked on?