Just to add some info to this long, old and detailed thread....
I recently purchased a used 2010 Mac Mini with the stock mechanical 320 HD. I was going to put a SSD in it, but had to wait until it arrived in the mail.
In the meantime, for experimentation, I wiped the HD with disk utility using the Snow Leopard startup DVD and partitioned the drive in half and installed Snow Leopard on one partition.
After that was fully installed & updated, I installed El Capitan on the second partition on the internal drive (that's why I got a 2010 Mac Mini).
During the course of playing with the Mac Mini with two new clean installed OSes and switching back & forth to compare..... Many times I get the "can't find startup disk" icon when booting up even though I previously chose the startup disk. And same as the op, if I hold the option key during startup and choose the disk (and wait a few seconds after choosing it) I can boot into the disk I want.
So in conclusion, (for other El Capitan users) the failure to find a startup disk is not related to USB, SSD, PRAM, SMC, or bad hard drive, but just the nature of the beast.