Will any error which causes the check engine light to go on show up as a DTC during a regular OBDII scan? This is obviously only in relation to OBDII compliant vehicles.
EDIT July 26th, 2016
So I just ran across this page for VAG-COM, which is software for talking to VW-Audi Group cars. On their page, DTC Comparison (Why a generic OBD-II scan tool can be useless) it says:
Here's a real-world example from my car from September 2002. My car (a 2000 GTI 1.8T) had stalled out several times over a period of a few weeks. One evening leaving work, the car stalled, but I was able to restart it. The Check Engine Light was not on, but I scanned for codes.
It then goes on to say that no DTC's showed up during a generic OBDII scan, but that ten proprietary VM-Audi codes showed up when scanned with their software.
This would seem to indicate to me that manufacturer specific codes don't set the CEL, although I guess this could vary from manufacturer to manufacturer.