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JB4 ISO is not completely pass through even on Map 0. Either log with JB4 or disconnect it to log with AP. Not sure why no boost, might try switching to DME boost control for the time being if you keep the JB4 in. I ran both when I first got my AP, took the JB4 out 2 days later and haven't looked back. You'll definitely want a custom tune with the AP.
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