Hi Clive
That is the way certification is meant to work, the courses that are in the primary certification are reset and are not required to be completed again unless they are also included in the recertification path
The first thing to check is that the recertification path doesn't have the 'Use the existing certification content' ticked.
if this looks Ok then check to see if the users has been unassigned and then reassigned to the Certification. If this occurs then the users will be placed back onto the primary certification path. See the reassignments docs for more details.
If this looks Ok then can you create a support ticket with details of the Certification settings, versions, recreation steps so we can look at closer.
regards