Yeah its fishy at best sometimes. You just have to really pay attention to what it says. Always check one night against your multi-night stays. Generally speaking longer stays will come out a bit cheaper. When they don't, there's GOT to be a reason for it. Here's just a few (my personal take, of course):
Room availability may be almost maxed out for one of the nights. Book two, and your rate is high - book one and it's lower. Keeping the hotel from going into a big oversell.
It's a holiday. There are no rules in life that apply to holidays...this includes room rates. Things get WEIRD when holidays are involved.
There's a convention in town. Lots of rooms one night, and no rooms the next for a hotel really screw with rates.
You're booking during season shift. Example - You book August 31st through September 2nd. August night is way more expensive because it's still "summer" - September is not, thus it's cheaper.
Those are just what's on the top of my head. I'm sure there's more. We run into them all the time.
Also keep in mind, rates that you find online and through 1-800 numbers are usually set by some Joe somewhere who's never even actually seen the hotel. Speaking directly to the property will often yield something a little different. But not always ;-)
And that's my 2 cents for the day! lol