Thanks for the bug report and investigations.
I agree with Hendrik that this is a bug that ought to be fixed because it leads to inconsistency.
But Pierre is right that this use case goes beyond the original PG simplistic queue management, which originally did not allow any UI steps forward/back once a queue was in progress, except to interrupt. Later I relaxed this to allow advancing the queue (it's easy to add more items), but I thought retraction was still forbidden (it's a bit trickier to do removal from the queue, even if only to avoid the item currently being processed).
So I am surprised that C-c C-RET is allowed in the above case, I thought it would trigger a UI beep/busy message.
Maybe some recent changes elsewhere for the multiple file handling inadvertently opened up this behaviour? It might be worth checking what happens in PG 4.0.
