Since the newest update most of my faction reputation was reset to neutral and now when I'm about to get higher than accepted with the NCR it resets back to neutral.
Is anyone having this problem?

Turns out my NCR combat armour was resetting them,,,,pretty annoying,,,

sometimes when you have faction armor/clothing on it will change the reputation people have for you on your pipboy. for example, if you put NCR armor on and have a good reputation with the legion, you can expect the words neutral or villified or whatever to appear under cottonwood cove and other legion places. I don't know if this was the problem you were having, I noticed it one day and thought "WTF?" but if you take the faction armor off it goes back to the reputation you yourself have with them.