Try using "Append Rule Name to Job Name" in Split.
Alternatively you can use the variable for the job number in the job group $FFwfDoc.documentSequenceNumber$ in Save. For instance:
I have a workflow that splits a PDF by pages, and then it saves to a specific location, but it's overwriting itself. I start with a 2-page PDF, split it into two single-page files but instead of gettting two files in the destination folder, I get one single page PDF.
I've tried this with splitting pages by segments as well and the result is the same.