This happens mostly with drawing objects, and to a lesser degree with shapes. When resizing drawing objects in Flash CS6 with pixel snapping turned on, one would expect the dimensions of the shape to snap to even pixel numbers. For the most part it does, but too frequently the position and size values begin to drift into fractions of pixels.
If you create a rectangle as a drawing object, no stroke, it will snap to pixels properly. Drag it around and it always lands on whole pixel values. Now try resizing it using the free transform tool, or even by clicking and dragging the position and size values in the properties panel. Width and height values will mostly stick to whole pixels, but too often it will slip into fractions of pixels, bizarrely offsetting the x and y values as well. If you resize a drawing object and this error occurs, it does not help to try and move it to snap it back onto whole pixels, because it will snap to whatever fraction of a pixel it's currently stuck in, thereby forcing the user to manually edit the object's x and y coordinates.
This is a problem in my workflow as I'm constantly having to keep an eye on the properties panel and manually editing the numbers when shapes stray into 2.85 pixels or some such when I want it at 3. I find myself frequently just entering the numbers I want, which defeats the purpose of pixel snapping in the first place.