I right-click the Scale value for a layer, select Edit Value, and in the Scale dialog box I choose Units: pixels. I note the pixel values for the width and height. I close the dialog box.
Then I hover my cursor over the edges of the layer and use the Info panel dialog box to calculate the width and height of the object. The figures there are much smaller than those in the Scale dialog box.
The values I calculate from the Info panel are correct. Those displayed in the Edit Value: Scale dialog box are wrong.
I noticed this in a project submitted by an AE student of mine. What's happened is that the layer somehow became smaller in appearance while retaining its 100% scale value. No effects have been applied to that layer.
The layer is a 400x400 TIF. It's placed in a NTSC DV comp. If I choose Layer > Transform > Fit to Comp Height, the scale changes to 120%, as it should (120%*400=480, the height of an NTSC comp), but visually it takes up less than half the height of the comp.
I figured this out. The difference in scale is due to the TIF layered being parented to a layer that had its scale reduced.