This is caused by enabling CONFIG_USB_LIBUSUAL=y.  Despite being
documented as a "module" when it was added (complete with the suggestion
of setting options in modprobe.conf), this is a boolean option.  So it's
built into the kernel, which means it doesn't get another bash at
coldplug after the root filesystem is mounted.

Please, can you disable CONFIG_USB_LIBUSUAL?  The reason for it is
CONFIG_BLK_DEV_UB -

"Low Performance USB Block driver.  If you enable this driver, it is
recommended to avoid conflicts with usb-storage by enabling
USB_LIBUSUAL.  If unsure, say N."

I can't imagine why Ubuntu needs this.  AFAIK the only reason for it is
to save a few K on embedded systems.  It might be interesting for
debugging purposes, but as this (and other previous bugs) have shown, it
seems generally more effective at inserting bugs into a systems that
should be working.

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https://bugs.launchpad.net/bugs/1062796

Title:
  usb-storage devices don't work, unless plugged in *after* booting -
  happens when setting MODULES=dep in initramfs.conf

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