The NN3D takes a looong time to load regardless of anything connected to it.
We once or twice had AIS targets disappear from ours too, but they always came back after a while. It has concerned us, but it has only happened so rarely.
Also keep in mind that there is a maximum distance in which the NN3D will display targets. If those targets move outside that distance, they disappear. Instantly.
This distance is user-variable, so you might want to check in the menu section that yours is not set unusually close.
If it isn't any of the above, did you try resetting the AIS instead of the NN3D? It may be possible that there is an NMEA error occurring in the AIS output.
Also, make sure that the AIS NMEA 0183
input is selected in the setup menu, and that ONLY the AIS checkbox is checked (and it is set to 38400 baud).