My son has tons of button down shirts in non-white colors. A lot are hand-me-downs so I'm not sure where they all come from but you might just be having seasonal problems - right now is not the best time to look for modest clothes for either gender. Land's End has the best quality dress shirts for little boys by far - I especially love that they come out of the wash ready to wear unlike the cheap ones that need ironing.
Girls' skirts are so easy to sew. If you are not finding what you want I would recommend making them yourself. Circle skirts, gathered skirts, and even some fancier faux-placket skirts take almost no sewing ability. Recently Land's End had women's petite button down dress shirts on sale and I grabbed a couple for $2.50 each to make shirt dresses that will come down at least calf-length on my little girl. It is really hard to find pre-made clothes that fit all my requirements but they do seem to turn up here and there. I'm just learning that I can't wait until we *need* a certain size to shop and I try to grab the good stuff when I find it.