Don't think it could be corrupt preferences. I've tried trashing the prefs as well as reinstalling CS4.
I've noticed that it has something to do with an object that has a stroke. If I create a new box without a stroke then then my initial measurements are correct. However if I add a stroke my measures change according to the stroke weight. I've looked for ways to turn this off, but can not seem to find anything. I think this problem has something to do with the over all appearance of things.
Which lead me to another issues I'm having.... What happened to the "Filter" menu? When I try to round corners on a rectangle it applies the round corners as an effect "appearance". I have to expand the appearance in order to the corners to actually be rounded. Why did this change? I want to change the actual object the first time I create it and not take extra steps. This can waste a lot of time. I think this same issue is what is going on with the stroke weight. I don't want my object size to increase when I increase my stroke weight. If I did want this, I would create outlines. Can this be turned off? If not, I will have to continue using CS3 until Adobe fixes this problem.
OK.... I just figured it out. Under Preferences and Align pallet menu, there's an option "Use Preview Bounds" that was on by default. If you turn this off, then all of the Aligning and scaling issues work just fine. Go figure...
That was a surprise: Use Preview Bounds was the first I thought of, but as far as I remember, it always results in larger dimensions. I will remember, and I apologize for not mentioning it.