Illustrator CS4 measurements and alignment issues

When I create any object to a specific dimension (say a square that is 5" x 5") the dimensions in the transform pallet are always smaller than 5" x 5" and never the same each time I create a new object. When I try to correct the size by typing in my dimensions in the transform pallet (width and height) the dimensions change but they do not reflect what I just typed in. If I try to correct the size a second time the dimensions finally reflect what they are supposed to be. I've been using Illustrator since 1988. I just upgraded to CS4 from CS3. I've never had a problem with inaccurate dimensions. This is a waste of my time. Can some one tell me why this is happening? Is this just another bug that has yet to be fixed? Or is there a setting that will fix this issue?
Another problem that I'm having is with "Aligning" two objects that butt again each other. For example... draw two boxes and align one side so that one edge is exactly on top of the other edge. Ok... I can do this by turning on smart guides and dragging one edge on top of the other. However, my problem is with the Align pallet "Distribute Spacing". In Illustrator CS3 you can select two objects, then select your target object to align to. When you click on distribute spacing in the align pallet the two object edges are perfectly aligned. CS4 does not seem to to do this anymore. Can some one explain why?
Just to be clear for those who like to read into things.... 5" x 5" is just an example. So pick a number. The dimensions are never correct.
I'm using a Mac with OSX 10.5.8.
Thanks!

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.

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