For a while now we have been working on eliminating duplications of swatches and gradients when these are imported or copy/pasted from window to window. While working on bug #1318657 I put in a change that also eliminates duplications of most gradients shown in fill/stroke when they are cut and paste in the same window. These changes were committed to trunk at revision 13417. I think the new behavior make sense but it is certainly going to look strange if you are accustomed to a huge number of gradients piling up in that list. For a better description see
https://bugs.launchpad.net/inkscape/+bug/1318657/comments/12
and also post 14 there.
Thanks,
David Mathog mathog@...1176... Manager, Sequence Analysis Facility, Biology Division, Caltech