Not so much of a 'how do I?' as 'why is this?'

Anyhow....

Backed up via cp a few days ago - individual tables added up to around 70mb.

Tonight backed up via phpMySQL ( Complete inserts, Extended inserts) and it was 40mb.

Just in case something had corrupted - I deleted the MySQL download and re-downloded 3 times - always 40mb.

Any thoughts on this?