Go to the office. I have NEXUS and had trouble on the Canadian side, I got IMM 1-1 (Immigration I, speak to a secondary officer) and each time they asked me a couple questions, said everything looked good, stamped my passport and sent me on my way.
Once I got a new work permit I went into the NEXUS office in Toronto Pearson and they said my expiring/expired work permit (it started sending me to secondary six days before my work permit expired) put a block on my NEXUS and they had lifted it. Fingers crossed that I'll get a normal reciept this Monday.
Regarding the passport page, my machine readable zone (text at the bottom of the passport ID page) is so worn that airport kiosks don't like it, which includes GE kiosks (where it will rarely scan). I can successfully scan one out of maybe ten times. I just click the button to find by document and punch in my passport number instead and everything works. Might be worth a shot to try that if CBP tells you everything appears in order on their end.