Heh, after reading the first post, I was about to say "sounds like it is trying to boot directly from the Windows disk". Good thing I read the whole thread before posting.
I've seen some BIOSes forget the boot order (and have this stick as a permanent change) when a drive doesn't appear during POST, or if an extra
drive (even an external USB one) appears during POST. So some possibilities:
1. Intermittent problem with one of your drive cables (most likely the one the SSD is connected to, but could by any of them).
2. Intermittent problem with the SSD that caused it to not appear during POST on the boot attempt where the boot order got flipped around.
3. You had an external drive (or thumbdrive) plugged in to a USB port during POST, and your BIOS is one of the ones that gets confused by this.