The problem is that walkovers do not necessarily give 48 minutes per position. What I've found from the forums and some experimentation:
Normally, the starter gets 36, the reserve 10 and the backup gets 2. If one player is set to starter, reserve and backup, he gets 43 minutes instead and five minutes are "lost". (This applies even if he's at three different positions, like staring SF/backup PF/reserve C, incidentally).
I found that a backup at two different positions (pg/sg in my case) will get 20 minutes, so no minutes lost there. A player that is a backup at 1 position and reserve also gets 12 minutes, and I had a guy backup one position and be reserve at two positions and get 14.
My best guess is that if a player listed as a starter is also played as a reserve or backup at any other position then he 'loses' five starter minutes, but I haven't had the opportunity to play a known walkover team since last season. In any case, there is some sort of rationality to this normally.
Of course, I have no earthly idea how you ended up with the minute distribution you ended up with. Maybe a blanked lineup? Or maybe the PL engine doesn't handle minutes on WO the same way since there's no training involved?