There are several places to change NX preferences:
1. Customer Defaults - this is only change the current session in NX
2. NX, Preferences
3. Seed file
Not know exactly what preferences that you were referring to, my assumption is that you are using option 1 or 2 to change your preferences, and next time when you launch NX, you have to redo those all over again.
Option 3 will make it more persistent, so next time when you launch NX, you will have the same settings.
However, editing the seed file(S) will also change those settings for everyone in your company, they will all be using that same seed file(S), so, it would required the following:
you might want to consider using a Macro to record all of your changes in your NX preferences. Then just run the specific Macro to get your preference reset, it is very easy to do.
Tools -> Macro -> Start Recording (quick key = Cntrl + Shift + R)
change your preferences and NX Macro will remember your selections
Tools -> Macro -> Stop Recording (quick key = Cntrl + Shift + R)
to execute the Macro, it runs through your recording very fast.
Tools -> Macro -> Playback (quick key = Cntrl + Shift + P)
I used this quite often whenever I have many repetitive actions in NX.
Let me know if this is helpful.