With root on an LVM VG that includes a USB attached disk, it's not possible to have mkinitrd 
automatically generate a working initrd image (it is possible if you manually specify the appropriate 
modules with --preload).

The problem is largely the small block of code that attempts to figure out whether or not the USB 
modules are necessary by explicitly checking to see if /boot or /root is on a USB attached device.  This 
test is far too clever by half, and in an LVM environment will never succeed.

Rather than trying to "fix" the test so that it works correctly, I think the best solution is to simply 
remove this test and have the "--with-usb" command line option simply cause mkinitrd to include the 
USB modules.  Trying to outsmart the sysadmin with clever shell scripts is generally a recipe doomed to 
failure.

I've attached a patch to mkinitrd that makes this change.