The NXE file is meant for Integration Tools like LonMaker and CT and should not be used with NodeLoad. The NXE file doesn't contain all the information needed for to fully update the device using NodeLoad.
Is the issue that the node is left in the soft-offline mode after Nodeload? If the image was exported configured, then this will be the case, but as soon as you reset or power up the node it will be on-line.
Additional FT 3120 information is available in KB982.