Not sure how to describe this but after starting NMM this morning 80% of my installed mods have the yellow triangle exclamation sign that usually indicates I don't have the latest mod version installed, however most of them now say the Latest Version is 1 even though I have version 1.2, or 1.6b, etc., installed. Last night I went through and updated a few that needed updating so I hope I didn't break something. Also my Windows 7 have a big update when I logged off last night so I am unsure if that is related. I was about to start a new play through this morning but am worried to launch if it might break my save files... any idea?

Probably just Nexus servers crashing or glitching out under heavy load. I wouldn't worry about it unless it doesn't fix itself eventually. It shouldn't affect your game in any way.