One other factor that I haven't seen mentioned above. With some receivers, on AC3 channels, it isn't enough for the receiver to just have the proper APID. The receiver must also know that the audio is AC3. On some receivers, the only way for the receiver to set the audio as being AC3 is to have it scanned in itself or, if the receiver has a capable channel editor, sometimes the channel editors allow you to set the audio as being AC3. Because of this, some receivers cannot do AC3 on manual channels where you specify the PIDs.
But anyway the point is, that if perhaps you have a poor signal, and when the receiver is scanning in the channels, it may get the PID correct, but due to data errors may not determine that the channel is AC3, or perhaps it may not have scanned in PIDs at all, and yout try to manually create the proper PID, but it gets set as type 3 MPEG instead of type 81 AC3.
My Coolsat 8100 sometimes gives me headaches trying to scan in channels off a weak transponder. Sometimes it misses channels, and when I create them manually, there is absolutely no way to create them if they are AC3, because the receiver assumes that they are MPEG.
Anyway, not sure if that might have been related to the issue here or not, but since a rescan seemed to fix it, it's possible.
