My guess is that it uses this sound as a backup when it can't access the ringtones you might have set from the sdcard. Since it prepares the card after booting, something must be causing it to ring (and resort to this "backup ring" until the card is ready to be used).
Either way, the sound is kinda annoying, but I thought it was odd the first few times I heard it as well.
The way I went about it, was to take the custom tone I use, rename it from .mp3 (or whatever it happens to be) to .ogg, then for simplicity sake, place the .ogg file on the root of your sdcard. Now open terminal emulator;
#mount -o rw,remount -t yaffs2 /dev/block/mtdblock4 /system
#busybox cp -R /sdcard/(tone).ogg /system/media/audio/notifications
#mount -o ro,remount -t yaffs2 /dev/block/mtdblock4 /system
Some ROMs will have a shortform to mount the system (i.e. mountsys, sysmount) it depends on what you are using, but those can save you alot of that typing.
An even easier way to fix this is to just use a stock notification tone... but where is the fun in that
Hope this helps.