Firstly, confirm I have the correct understanding. One is punctured by tightening the end cap and other is punctured by a moving piercing pin in the valve? And the one at the end cap is getting pierced while the one at the valve is not?
If so, here’s what may be happening…especially if you’ve tuned it to use CO2 more efficiently. The one punctured by the end cap happens first. That step pressurizes the tube. This pressure resists how far the hammer knocks open the valve when you fire it. If the valve lift is insufficient, the piercing pin in the valve will not reach the other cartridge to puncture it. At least not until the first cartridge is so low that the POI has already fallen to the point where you open it up to change them out.
To see if that’s it, insert a new cartridge first and load an empty one second. Dry fire a few times and see if it punctures it.
Other possible causes are easier to explain but will require disassembly to check. Perhaps the piercing pin has a broken tip (usually hardened steel, so somewhat brittle), or it’s simply too short, or there’s a burr or other obstruction preventing it from coming through the end the valve.