The only mods that "should" ever be throwing that warning are Core Mods and there are only 6 of them in popular usage. Even then, the game shouldn't be crashing like that. There is no difference in the game files between Patches 1.66, 1.67, and 1.69. If a mod is made for any one of these, it will work exactly the same on the others and the updated Core Mods really only account for the new internal build numbers. Where this used to be critical was back on Patches 1.63 and prior or with attempts to use Core Mods intended for the prior patch levels on a more up to date game.
For the list of Core Mods and which ones have 1.69 versions:
http://nraas.wikispaces.com/Patch+1.69
Script and Tuning Mods, CC, etc., require no updates or special versions between these patch levels.
If you are getting the core version mismatch warning with no Core Mods in play, or you are certain with only those made for 1.69, not multiple copies, not packages merged together, not Steam versions, and not running with stale cache files, then that I'm afraid leaves us with the possibility that you have a broken install. What happens if you try to run the game with no mods at all?