I'm leaning towards lean fail-safe that's built into the JB4; everything that you described indicates that it went into a fail-safe protection mode.
What is your OL setting at? Can you email or post your logs for us to view?
E90 LCI M3 7-DCT Interlagos Blue/Novillo Silver
[MS Pullies|K&N drop-in|Test Pipes |Evolve Stage II tune|Evolve Servo Map|Evolve M3 GTS-DCT file]