The gutter text lines do not align with the text lines of the text area when extra vertical spacing is configured. See the screenschot in attachment, there is a (in my case) downshift of the gutter. Since it is a constant downshift, that does not accumulate N pixels for every line, it is not much of a bother, still it's a bug :)
Using jEdit trunk snapshot 2012-06-11_12-02-24. In the screenshot, i'm using Look&Feel, but I've retried without the plugin and the downshift is still there. (by the way, if that matters, I'm using Consolas 10 pts in the text area and Consolas 9 pts in the gutter, Windows XP)
I guess that, since every gutter line has to be synced with the matching text area line (and since font vertical size is different), a "vertical sync" is applied independently to each line. Which means that this "sync" does not apply extra vertical spacing - which should explain why the downshift does not accumulate.