This problem should not be occurring as the SCALE algorithm will maintain the NO_DATA_VALUES. Please make sure you are using the most recent version of Geomatica - Banff: https://www.pcigeomatics.com/trygeomatica. This could be a problem with your specific dataset. If you continue to get the same problem when using Geomatica Banff you can contact email@example.com and they can assist.
Hope this helps!