Bootmii only functions from the power/reset buttons on the console or a GC controller. A similar app is Priiloader, but it isn't nearly as effective as bootmii installed to boot2 and doesn't allow you to make a NAND backup.
Burned discs only read at 3x in the console, whereas normal discs read at 6x. This may be why you're experiencing noise issues as the laser is working harder to do the same job. For thoroughness, usb loading reads at 8x.