I can offer a couple of answers from experience. Yes, damaged pellets at loading can result in this behavior. And yes, pellet clipping can be intermittent, but you have already seen the same behavior without the silencer, which seems to rule it out. A dirty barrel can behave in this manner too. It could have fouling that requires more aggressive cleaning. Loading single shot could suggest a faulty magazine if pellets are being damaged at loading. I would first do a chrono run and check for consistent velocity. A dirty or dry hammer can cause this result (this will vary, check with maker about lube). I don't believe you mentioned how much you have shot this rifle. It could simply be a bad barrel. I had a Red Wolf barrel that shot this way, and it turned out to have a couple of machining imperfections that was damaging pellets. Compared to cartridge rifles, air rifles have so many variables involved, trouble shooting can be frustrating.