I understand what you mean...Let's have a look.
Left: Toshiba 4GB without U3 - 3.72GB
Right: Sandisk 8GB Cruzer Micro flashed with a 644 MB ISO image using universal customizer - 3.01GB
I have had the same problem with my 8GB cruzer micro.
The 3GB problem is very likely to be caused by the universal customizer.
I've recover the lost space after uninstall/reinstall the U3 with the offical software from sandisk.
U3 launch pad removal