It seems that the slider thumb is resized by the trough border when painting. I don't see this happening in the GTK+ sources and removing this resize re-center the thumb.
Created attachment 115956 [details] Patch
Comment on attachment 115956 [details] Patch Ok!
Comment on attachment 115956 [details] Patch Clearing flags on attachment: 115956 Committed r103945: <http://trac.webkit.org/changeset/103945>
All reviewed patches have been landed. Closing bug.