You say the round in the chamber is live so what could be happening is
1. The old round fires and ejects fine
2. As the slide goes back, a round pops out of the magazine early
3. As the slide comes forward, it picks up a round like it's supposed to
4. The second round lodges behind the first, because it has nowhere else to go
2 could be caused by loose mag lips (like when I used a 40 mag in a 9
) or the slide bangs against the frame at full recoil and the shock bumps a round out of the magazine or something along those lines. Either way the magazine is probably at fault, either fully or partially.