It reminds me of one of the early Topfield PVR features where during boot-up the OS didn't wait long enough for the HDD to spin up from cold. Cured, I remember, by the simple act of adding a extra small delay before attempting to read the disk during the boot process. Perhaps with 2.5 inch disks and slower startup-ups for green drives the timing is marginal for some HDDs?
I've recently put back a USB memory stick into the mix. When the internal HDD (2.5 inch, 1TB fitted by the sponsor) goes missing the USB stick is always found.