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For your first question, the screens missing from the list probably aren't public - it wouldn't make sense to let other programs open their windows on screens that might need to be closed again soon, or where all the pens are used up, as in Multiview's case. Private screens won't show up on the public screens list.
And the second question - the program is stuck at the WaitEvent command and isn't actually running, which is why the debugger can't stop it. WaitEvent suspends the program and waits for an event from the OS, so if there's a window on your program, you can trigger an event by clicking a gadget, moving it, whatever, and then the Stop from the debugger will take effect. Without that however, it's a dead process and you can't do much about it.
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