If you have your Pixel aspect ratio correct (which is what Vince suggested you check) you might also be running across the problem that, while 16:9 HD really is 16:9, where as 16:9 SD isn't actually 16:9...
Because the aspect ratios are slightly different, you can get black bars.
There was a thread on the cow a few days ago about this, and Vince posted this link, which explains the problem:
http://www.mikeafford.com/blog/2009/03/pal-d1-dv-widescreen-square-pixel-se...