Thanks I found that (and wish I hadn't, lots of errors!). I grabbed gerbv from source forge which displays the gerbers I should still have a kicad copy around so I'll probably try that too and see which I like better. Oddly enough the 300mil diode seems mostly OK. Thats odd because the 400 and 500 mil versions are a simple clone with the pads moved but at least the 500 is broken. When I moved the stroke and stroke-length back in to connector0pin and connector1pin with Inkscape xml editor it leaves them there but the square pad on pin 0 is now overwritten because the pads have become larger for some reason. I'll continue poking at it and see if I can figure it out (and go back and look over all my previous parts for problems too ...)
The extra groups are sensible for more fancy PCBs, its possible they just didn't need the function for this simple a part but put the layers in anyway.
(edit) This keeps getting weirder! I just Inkscaped the apparantly working 300 mil part and it is identical (as it should be) to the 500 mil part except for pad spacing. It has the same stroke and stroke-width in copper0 but not on the connectors but it appears to work correctly (at least as far as I can see). Nope, the holes (when I remove the copper layers) are the larger size for the 300 mil and 400 mil too so it looks like the stroke thing is a problem and I so far haven't found a fix. Keep trying I guess.
Peter Van Epp