Welcome in my world 🙂
I've got 4 2009 Mac Pros - in 4 of them I've done successfully update do 5,1 - and in 4 of them update to High Sierra (which means genuine Apple Firmware online download applied).
In 3 of them RAM is running on 1333MHz - in one...... 1066MHz :/
I've done RAM swap - nothing.
Obviously everywhere Xeon supports 1333MHz RAM - I even swapped whole CPU trays - nothing.
Crazy thing how this one is different is... the one which was dual socket tray (12 core) (MOTHERBOARD!!!) does not working under 1333MHz - I said motherboard as..... when I put that dual socket tray to..... genuine ONE socket.... MOTHERBOARD - it is showing.... 1333MHz.
The only thing what comes to my mind - Apple is releasing different firmwares (I know they are the same number) but as I KNOW - doing upgrade Mac Pro 1,1 to 2,1 - there are two the same - but DIFFERENT firmwares for..... refurbished Mac Pro - and non-refurbished!!!
Madness - but this is how Apple is doing.
I'm wonder what would happen when downgrade to 4,1 - BUT SINGLE CPU tray in dual CPU MOTHERBOARD then flash to 5,1 again - and flash again doing High Sierra update.
The thing is stopping me to try this it is that genuine Apple firmware applied when High Sierra update - if there would be no that update - it is safe to downgrade - with that different firmware.... well - who knows - anyone wants to try? 🙂