I am having the exact same problem you are having. I think the problem comes from uncertainty about how we will play future streets.

What I think goes on in our heads is this. "I think he has a draw which I'm a coin flip against but my two pair doesn't look that great on almost all turns (only 2389J are safe cards in our minds) so I will just stick it in now and gamble it up."

Also I think we believe we will make a mistake on 5 and 6 turns because we don't know if that hits his draw as he doesn't always have the lower end. It really comes down to how aggressive someone is and how hard they will push their draws even when they miss but a potential dangerous nut hand comes out such as 5 or 6 but they still fire pot. Then we get scared we will sacrifice the pot sized bet on the flop plus the potential future value of the best hand from calling bluffs so we go FUCK IT SHOVE!

I almost always make mistakes in this spot when I shove and the reason is the player leading pot almost always has us dominated or coin flipping. I think the prudent play is to just call when this deep and PLAY POKER. Its tough, especially when a card like an ace or king rolls off and he still mashes pot, but c'est la vie.