I can confirm that this is from one of Penguinbait's automated SD clone-and-bootmenu packages; it plays after the SD filesystem has been successfully checked.

After any crash or unexpected shutdown from an ext2-based cloned system, you should reboot from flash, and wait till the check is completed, to avoid corruption of the filesystem; the sound serves the useful purpose of letting you know when it's complete, and you can reboot to the SD. (If you convert to ext3, which is journaled, this fsck is not necessary at all...)

As for removing it, Penguinbait has posted specific instructions somewhere about...
*points to search*
(I'd tell you if I knew, but I've never actually used any of PB's SD packages.)