there are a few relating to the nano upgrades.
1 is you need to get over 1000 nano points b4 any register and can be used. another is you loose all your nano points if you restart the game from a current save. (you die with 2000 nano points and decide to quit, later reload the game, start where you left off but the nano points you had are now gone)
have you patched up to 1.1? coz that makes no diff. 1.2 will hopefully fix em though.