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VW has 3 sets of ignition timing tables.
  • Base (main ignition set point)

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  • Minimum

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  • Reference Tables

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The reference tables are used

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as a benchmark of the optimal timing assuming optimal conditions and no octane limitation.
The reference tables have additional correction tables (which appear to be identical to the correction tables available for the base tables).
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The final result of the base ignition timing value after corrections is subtracted from the final result of the reference ignition timing calculations to form IGA_DIF
That IGA_DIF value gets translated here into an ignition efficiency value here. The x-data and y-data here are swapped due to the way we extract data from a2ls currently. 
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The output of these tables is the value we get for the monitor Ignition Torque SP Efficiency Vlft High/Low

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Ignition Torque SP Efficiency Vlft High/Low is

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The solution here is to make the reference ignition timing values and your base ignition timing values closer together so that the value in iga_dif_av will fall into an area with less of a penalty to the torque values. A value of -13 to -17 in iga_dif_av will have a 9% change to the torque value at most. 
I have some idea of disabling this system (once I can get the XMLs working again). Last time I was messing about in this area however we removed ALL torque reduction, which was not good for the DSG shifting at full throttle. 

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then multiplied by the value from the Reference Indicated Torque map. 
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The system is intended to correct the reported torque value so that it is an accurate representation of the torque output from the motor, but can clearly cause some issues when calibration values start to differ by a larger amount.