Common causes from N54 tech
The first is the over-boost safety. If boost exceeds the value you've set under user adjustment the SES light will flash once and the JB4 will switch itself to map 4 until you restart the car. The default setting is 18psi. Common causes for this are setting the value too low for the map/intended usage, improperly configured or defective wastegates, or JB4 setting problems.
The second is the run-lean safety system. If your air/fuel ratio (either bank) runs leaner than 14:1 over 4500rpm for more than a second the SES light will flash twice and the JB4 will again switch itself to map 4 until you restart the car. Common causes are maxed out fuel trims (see E85 notes above) or o2 sensor faults. Note any o2 sensor fault must be corrected for the tuning to operate properly.
Another commonly triggered fault is low fuel pressure. If your high fuel pressure drops below 7 (~800psi) the JB4 will flash the SES light three times and switch to map 4 until you restart the car. Common causes are an inadequate low pressure pump, too strong of an E85 mixture for your tuning/fuel pump, or a failing high pressure pump.
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There is also a function on the JB4 to keep DTC off all the time.
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