Try setting IgnitionOptions - Wheel Decoder Routine to "025 Style"
I'm sure hoping it's set to 024s9 Style, which appears to have very little tolerance for extra tach pulses.
[There also looks to be a code bug in 025 where the ~2x missing tooth period is included in the average tooth time calculation without dividing it by 2 first, but this is still better than the 024s9 style that doesn't do any averaging and uses simply 1.5x the previous tooth's time to determine that the current tooth is the "missing" tooth on the wheel. If you get a noise spike in the 024s9 style, the next standard tooth can pass the 1.5x criteria and be mistakenly declared as the "missing" tooth.]
For logging, can you run with a Tooth Logger interval of 500ms or 750ms, instead of 250ms? I'm guessing that the logging code isn't interlocked and that too frequent of an interval can sometimes result in a single screenful showing both new and old samples from multiple different non-sequential revs.
If the logging and tach signal are working correctly, you should always see 2 or 3 long teeth per screen. [It looks like a screen is 93 events and, with a 35 tooth wheel (1 missing), it will show ~2.6 revs. Depending on starting time/tooth, it can cover 2 or 3 missing teeth.]