I'm having the same issue. For me, the problem started when I switched from a Sprint-specific ROM to Viper ROM (intl base). After 2 minutes of bashing my phone against the terminal at McDonald's, it did finally work. But it is not working instantly like it used to, and it acts like nothing is happening. I know it's not McDonald's terminal because it happens at another McDonald's and Walgreens where previously it was working fine. Tapping my phone to another NFC phone works so NFC itself is working.
I don't really feel like going back to a different ROM over this, but it is annoying.