Gun Misfire

It would really help if we new what kind of marker you were using.  Knowing the propellant source would be good as well.

Without knowing that, I will say the following based on the assumption you have some kind of Tippmann product, the power tube and valve were after-market products and you are using CO2.

There is generally no valid reason to upgrade from stock Tippmann internals.  In many cases any performance gains are so minimal as to not be worth the additional expense/effort of upgrading.  In some cases the after-market internals can cause malfunctions.  If the original power tube and valve were not  damaged, try reinstalling them.

You state that you "need new valve bolts" which means you probably have a 98.  If the bolts are not in place, movement of the valve could result in the problem you mentioned.

Teflon tape should not cause any problems as long as you got a good seal.  I prefer teflon tape to thread sealant because it is easier to control exactly where the tape goes and there is no waiting for it to dry.

If you are using CO2 (especially in cooler temps) it is quite possible that you are firing faster than the liquid CO2 in the tank can convert to gaseous form.  This results in steadily decreasing output pressure until there is insufficient pressure to recock the marker.

You mention having a Flatline barrel so I will add the following:  Some later Tippmanns need a heavier spring in order to achieve acceptable velocities with the F/L.  The additional length, rough inner surface and the fact that the ball is in constant contact with the top of the barrel all combine to generate more friction which has to be overcome to achieve/maintain firing velocity.