Hello-
  Without seeing your files, it is hard to provide a clear solution. However, recently Philips have started to save images in the order they come off the reconstructor, rather than the order they were acquired or a spatially contiguous order. This required a new version of dcm2niix. Do also note that Philips have deprecated PAR/REC, so I would recommend saving Philips data in the enhanced DICOM format. Regardless, I would hope the latest pre-release of dcm2niix will read your old PAR/REC files fine, and if they don't, you should post an issue on the dcm2niix github web page. 

You can get the pre-release of dcm2niix from here
  https://github.com/rordenlab/dcm2niix/releases
I will make a new stable release once someone sends me a Philips DTI validation dataset - I do not have access to Philips hardware, so I am at the mercy of users to report issues and provide examples.