Never seen any of that. And I'd have to question all of it unless I diagnosed it myself. No offense. I know you're a smart guy. I just don't take anyone's word for anything when it comes to diagnosis. No diag guy worth their salt should.
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You have HP Tuners, right?
Do this. Post the tune file from the original (broken) ECM, and a short log file. The log can be as little as 10 seconds of nothing but key on engine off, I just need to see the 'Details' tab. Then do the same for one of the freshly-SPSed ECMs, tune & log.
OK here is the update.
The original ECM definitely failed-EVAP Vent solenoid circuit failure P0449. It was stuck "on" in the ECM.
The replacement ECM programmed with latest calibration was actually a success even though it ran bad. Vent solenoid ckt working as designed.
The problem I was experiencing, the reason I questioned the SPS programming, was apparently related to DOD. So I started looking into that.
The final, main issue, was that I failed to notice the DOD had been disabled in the bad ECM. Car owner had no idea. Licensed the thing and disabled the DOD.
Summary. Turned out to be a simple thing after all. Maybe this lesson learned will help somebody else in the future.
If the first post had been:
"Hey guys, got this thing where it runs on this tune file (file#1 attached) but doesn't on this tune file (file#2 attached). What's up?" and somebody opens the two files in Compare and looks at Comparison Log and there's the answer right in the first reply.
Yes that is ultimately how I figured it out. This was supposed to be a straightforward repair. Not a tuning issue. Turns out it was both.