I think there's two possibilities here:
1) You are now renaming your images on Ingest and you weren't before. Since the sequence variable increments every time a file is ingested, files the first card you Ingest will always have lower numbering than the second card you Ingest if you are renaming with the sequence variable.
2) You were previously shooting both the RAW and JPEG to the same card, in which case Photo Mechanic would rename the pairs with the same sequence value.
As far as we know, Photo Mechanic never ingested files the way you are describing that it used to, as it doesn't really have a way of knowing that the images from one card are the same as the images from another.
If you'd like your RAW and JPEG files to get the same file name, I would recommend Ingesting them both to the same folder without renaming during Ingest, and then doing the rename operation after the fact.
