Tubing must always be flushed after cutting. Even if not cut in your shop; it was cut before it came to you. Chips, burrs, dirt and other contaminants have collected inside your tubing and drilled passages. These contaminants can cut device seals, damage valve sealing surfaces, cause erratic operation and reduce service life if not cleaned prior to fixture start up.
The use of improper fittings can also cause obstructions and restrictions. Some people have adapted fittings, which they had to use in SAE ports. Yes, the threads are the same on SAE and JIC flare fittings. The body length may be different. In one case the use of JIC fittings in an SAE port made a metal to metal seal at the bottom of the device inlet port. Obviously the "clamps didn't work." Be sure you haven't created obstructions by using non-standard parts.