I set up a 55g NPT about five weeks ago and my water was also cloudy for a couple weeks. Like you, I left my filter running with just floss installed and you could easily see it getting clearer every day. Whether that had anything to do with the filter or not, I can't say.
I've initially used filters on all my NPTs, mostly for water circulation simply because that's what was sitting around, but I've certainly had my share of cloudy water. I suspect some soils "soil" the water more than others and mine is one of them. That said, it sure has been good for growing plants!
Hope this helps,
Jim