How to diagnose startup lag with OSX 10.8 in a dual HD/dual-boot environment?

How to diagnose startup lag with OSX 10.8 in a dual HD/dual-boot environment?

Context:
I have a 2013 MacBook Pro with OSX 10.8 installed on the internal hard
drive. I have a thunderbolt external hard drive, with a second install of
OSX 10.8 on it. I use the latter at work and the former at home (there is
a silly, letter-of-the-law company policy that mandates that I use a
second physical hard drive for all company data, and simply installing a
second bootable environment on it seemed the most thorough way to enforce
that separation), so I switch between them a lot.
Problem:
When I boot one of the hard drives, and the system's last boot/shutdown
was on the other drive, there is a very long startup lag (sometimes more
than a minute, when normal startup times are under 15 seconds for the
entire boot process). It only occurs when switching between drives: I'll
boot onto one OS, shut down, start the computer, hold down ALT/OPTION, and
select the other drive (or sometimes simply disconnect the external drive
and let it auto-boot to the internal drive), and then the system will seem
to hang for around a minute.
The lag occurs regardless of whether I have physically
disconnected/reconnected the thunderbolt drive. Both copies of OSX are in
verbose startup mode, but the lag occurs before diagnostic startup output
is written to the screen (after the chime, but before the apple
logo/verbose boot information appears, during the initial grey screen).
The activity light on the external drive displays minimal-to-no activity
during this waiting period. Regardless of which drives are connected,
rebooting the system (which automatically boots into the OS that initiated
the reboot) is as fast as it should be, and exhibits no lag.
What I've Tried:
I've tried zapping the PRAM, and done a bit of googling re: EFI logs to
try and figure out what the pre-boot environment is doing during the
period of lag, but to no avail. Others experiencing similar problems are
typically having difficulty getting the system to recognize one of their
drives in the frist place, but that's not the case for me; I can see both
drives in the ALT/OPTION boot menu immediately, and it is only after
selecting the drive that the system did not most recently boot from that
the lag occurs.
Question:
What's going on? Where would I look for diagnostic information on what's
going on during that pre-boot phase? I'm reasonably technical, so
installing new EFI systems/bootloaders is fine, provided there's a good
reason for doing so.