Well my car was having the flat spot issue too.
Skoda Octavia vRS, K03s Turbo, Revo Stage 2+, Miltek TBE, Autotech FP, Neuspeed Turbo Outlet, EVOMS, S3 intercooler B9 T7 F6 (As recommended by Revo.
I decided after reading David's post i would go out change my settings to B7 T5 F9 do some logging and see what happens.
I was shocked to say the least. The car now pulls a lot more cleanly and from logging it appears to be making more power on B7 T5 F9 (working of the Air Mass g/s measurement) On B9 T7 F6 i had timing pull of around -2.3 to - 3 on a couple of cylinders through the rev range.
Whereas now there is no timing pull whatsoever and the car is making more power despite having less boost.
Have a look at these logs
Very healthy from what i can see
So maybe the best settings for a Stage 2+ car are B7 T5 F9
Carl