When you are running of the disk regardless of the loaded they all read the disk at 3X.
Because thay are reading at 3X you will always get LAG........
To run a usb loaded you dont need a HDD you can use a usb key
here is the one that I use
Configurable USB Loader...
Backup launcher 0.3 gamma is an old program and all users are now using NeoGamma r7 to load from disk
Go here http://gbatemp.net/index.php?showtopic=158884 for more info