Hello Peep,
I reviewed "for%20recording%20triggerlog.vemscfg" it should be configured correctly to flag both primary and secondary trigger, the only thing i can think that would cause improper behavior would be forgetting to power cycle in between changes (but you already stated you customer did that), strange ...
Has your customer already tried swapping secondary VR+ and VR- at sensor side to verify VR polarity causing the issue at 3000 rpm (with his normal "v3.3_u009985-A-2015.06.24-21.17.31.vemscfg" config back in place) ?
Best regards, Dave