As you have already noticed, synchronization doesn't work with file level cloning mode; it requires block level.
Synchronization uses a driver that tracks the writes on the source (called bitmap driver) and VSS snapshots. During synchronization the full cloning of the volumes has two parts: first a plain full cloning takes place, then the bitmap drivers starts tracking, then a VSS snapshot is taken, and an incremental cloning is done from that snapshot (in order to guarantee data consistency). This is "InitialSyncCatchUpTask" you see in the log.
It is possible that the NFS share has somehow interfered with the normal working of the bitmap driver (this has never been tested if I am not mistaken).
Please upload the agent logs from the source machine, there might be some hints there. They are in "%ALLUSERSPROFILE%\VMware\VMware vCenter Converter Standalone Agent\logs".
Regards,
Plamen