If block level deduplication is used (e.g. Windows Server 2012, NetApp), many of the blocks within each of the processed files will be the same, so these will be picked up by the deduplication software.
Identical files optimized by NXPowerLite are not always binary equal, so file-level deduplication will not always see files processed by NXPowerLite as duplicates.
Running NXPowerLite on your files will trigger a lot of activity from the deduplication software, especially for the first cycle. Subsequent cycles should see this activity decrease dramatically.
We recommend running NXPowerLite for File Servers when the duplication software/solution is disabled, or in case of adding a large amount of data or new system, running it prior to the deduplication process. This will ensure that the two processes are not competing for resources.