Slower load time if using copy with preserved atributes

I've notice something strange that I can't explain.

I SSH into the server and made a copy of a "/public_html" by using the "cp" command with "-pr" to a different location. and moved the original "/public_html" to store in a new location.

The weird thing is when a I "mv" the new ly copied "/public_html" and put it in place of where the original is. The site loads significant slower.

If it is an exact copy with the same attributes it should make any difference in load time. Is there any explanation for this?

Thanks.