Yeah JIC flare and NPT fittings aren't compatible with each other, you definitely need an adapter of some sort. Here's a fitting thread chart I found a while ago that should help you out.
Well what kind of fittings are you using? It sounds like you're using compression fittings. I know a lot of people have problems getting them to seal, and that's because you should never use pipe dope or teflon tape with them. I always recommend this guide to installing compression fittings...