Hi,

I want to compare 2 wav files, I would like a program that reports the amount of different samples in a file & time positions too. EAC, CDex, Audio Grabber all have a file compare feature but not exactly what I'm looking for.

I could use EAC & manually subtract the end by the start of all different positions but this would be a lengthy process.

Try Foobars 'bit compare tracks'

You can quickly find the position of the differences with a wave editor. Open the two files, and tile the windows horizontally.
Then copy one of the files into the clipboard, and substract it from the other (special past / mix / invert data). Or if your software can substract, invert the file before copying it.
Then zoom vertically the substracted file until you can see the first digital step out of the zero level (minus infinite db).
Now, you can see the differences in the substracted window, and, applying the same horizontal zoom to the original window, check the other file for the real signal at the difference place.