Lesmor -
Couple of things, I wouldn't engage any picture enhancement modes (such as super white... deep blacks... etc). Also, make sure you turn off any of the picture motion interpolation modes (not sure what epson calls them, but they're clear-motion modes).
In terms of the of the clipping patterns, your projector might clip. That's totally normal. I owned a JVC RS45 that would clip on those patterns. Are you viewing the patterns in a perfectly dark room? Did you go back and confirm that you set contrast correctly?
First, I'd go back to the contrast pattern and make sure you have that set correctly... then head back to the clipping pattern. You can always try a few little tweaks to contrast at the clipping pattern... if you aren't seeing an change, it could be that your projector isn't capable of displaying a full range of all color channels. No biggie - that doesn't mean you'll have a bad image or feel like you're missing out (visually speaking). Just take your time, double check your contrast and brightness settings and tweak everything as close to ideal as possible.
The best thing you can do is go through calibrating with the disc, then check some reference images that show flesh tones (faces, arms, etc). I can't remember if the SM disc has reference images, but the human eye is particularly tuned to recognizing skin/flesh tones that look unnatural or sickly. So definitely check to to make sure flesh tones look good. Then take a stroll through some of the other reference images to make sure shadow detail, blacks, etc, look solid.