Okay so this one is a bit different, or its just that I cant find anything on the same problem...

The vehicle is an AE86, however regardless of this problem... It is powered by a 16 Valve Bigport with Cams, Cam Gears, ITB's, blah blah. Originally it was running the standard ECU and an SAFC for the throttles and big injectors, but running like a pig and had 50 degrees of advanced timing to make it run, however startup was not easy... At this stage it made 89 Hp on the dyno and we discovered timing was retarding instead of advancing ( Hence all the Timing added in). I had the same problem with another 16V of mine which turned out to be an incorrectly set TPS. In this case the SAFC didn't get a TPS reading and suspected the ECU didn't either. At this stage we decided to get rid of the SAFC **** and went to MoTeC, twin coils and a dual output igniter. At least now we can see the timing mark but the timing still goes backwards, if we lock the ECU at 20 degrees, theoretically it shouldn't move at all, nek minnit timing retards to about 5 degrees after. Which leaves one thing - Somewhere, somehow the engine is mechanically retarding the timing. So I volunteered to make the 400+ KM round trip to my old folks place and grabbed my dizzy from my 16V to see if it was a sensor problem, put it in and rewired to suit MoTeC, still the same problem. I'd suspected it could have had a sheared keyway on the crank but that wouldn't give a consistent retard upon revs...

Can anyone share an opinion as to what it could be?

Thanks, Aidan

Doesn't your tuning software have selections for timing advancements? Are you positive it's set correctly? Sounds stupid so no offense but there's been some issues I've had that were the easiest fix I couldn't seem to wrap my head around.

Yes we can set all the timing ourselves but the problem is it somehow mechanically retards, like I say, we lock the ECU at 20 degrees (therefore the ECU no longer controls timing) and theoretically it shouldn't move at all, but somehow it still retards... It is possible to tune around it and add our own advance timing to every percentage of throttle movement and engine load but is very time consuming and not really worth it.

Check if there is any play at the timing belt crank gear as well.
A few millimeter of play over there can mean a huge difference in timing at the camshaft.

i had a similar problem where my stock 16v had high advance timing at 35 degrees, would go not go lower, Crank was off by a tooth
check for TDC, make sure Cams and Crank are lined up, Also since your there, check your timing belt

I've only worked with MegaSquirt but there is a feature to correct the issue you're having. MS calls it "hardware latency", or it accounts for the time for the signals to pass through the conditioning circuits. It's likely not a mechanical retarding of the timing but the ECU not accounting for the signal processing time.

Yes you can just tune the ignition table around that and have the same power output results. Your timing table will become more and more artificially high as RPMs increase. This is also why I recommend to think twice before using someone's basemap. Where your ECU will be tuned to your specific engine on a dyno, if you were to share your tune with someone else and not let them know that extra 5, 10, etc.. artificial degrees may damage their engine.