Certification settings of engine not resembled by OPT most likely the cause for discrepancy in OPT.
Essentially, OPT is as good as the Administrator makes it.
The Administrator can select certain selections for the configuration of OPT to ensure conformity for calculations.
If any discrepancies are found, these should always be highlighted to your OPS department or even better your EFB Administrator who can liaise with the OPT Administrator the findings (could be the same person in your company).