I don't think it's because your knitting continental, you'll notice that Amy also knits continental and hers are fine. I had a quick look at your problem, but it's a bit hard to identify, is there any chance we could have a closer look at the short rows in question. I can see from the pic on your blog that they do look funny, but I can't actually see the stitches in any detail to see how they are being picked up.
You could also try these links - Nona has a few different ways to short row, and you might want to swatch them and see if any of them work for you. There is the [COLOR=darkorchid]Wrapped Short Row[/COLOR], the [COLOR=darkorchid]Japanese[/COLOR]and the [COLOR=darkorchid]YO[/COLOR].