if you create a normal rectangle and apply Effect -> Stylize -> Round Corners... instead of using the rounded rectangle tool, you will have a live effect applied that will stay true as you resize your rectangle.
If you need your settings to remain proportional to the shape, make sure you have "scale strokes and effects" turned on. (in the flyout menu of the Transform panel)
And the best part of all, if you look in the appearance panel, you can click on the round corners effect to change its parameters.
The best way to avoid this would be to use the direct selection tool (shortcut "a") to select the two points on each corner you'd like to move, then move those whichever direction you'd like. As such, your relationship within the pair of corner points stays the same, while the boxes area grows. Hope this helps!
If you are on Illustrator CS5, you can convert your Rounded Rectangle into a Symbol & while creating the symbol, choose "Enable Guides for 9-slice scaling". You can position the 9-slice splitters in the symbol edit mode in such a way so as to exclude the rectangle's corners from scaling when you scale the symbol.
Presuming rectangles with rounded corners you already have, or wish to use, with vertical/horizontal sides, you may (using the Direct Selection Tool and having the Transform palette/panel open with the appropriate Reference Point selected):
1) Select the two sets of Anchor Points (the two rounded corners) to move (you may drag across them all);
2) Object>Transform>Move (Ctrl/Cmd+Shift+M) by New dimension - Dimension in the Transform palette/panel (W or H).
1) and 2) may be done both ways, of course.