The version of dcm2niix you were using is from 2022, before the PET BIDS specification existed. I would urge you to use the latest stable release

  https://github.com/rordenlab/dcm2niix/re...

typically, the DICOM images do not contain all the information required for subsequent processing, so you may want to use the PET2BIDS wrapper for dcm2niix

  https://github.com/openneuropet/PET2BIDS

The variable slice issue either reflects your data was acquired with variable distance between slices (common in CT, virtually unknown in MR) or that some slices are missing. Visual inspection should help you distinguish between these. I would check the provenance of your images and ensure that you have all the DICOM files, as missing files will cause issues.