I'm not quite understanding your problem.
So from what you've said, you've feathered all four engines, but you don't see all four feathered? Remember, you must shut off the engine before feathering.
There possibly can be such a limitation since stopping the engine before feathering (in typical scenario with the plane flying since there's no real reason to do it on ground) since it'd be impossible to stop it before ...stopping it. Feathering can be done on a running engine.
If by "shutting off" you didn't mean stopping but one of the following: shut fuel valve, mixture cut-off or magnetos off (all all of them combined), then it's closer to reality. Of course just throttling back to cracked throttle does basically the same (what little combustion is left shouldn't cause detonation, etc.). It might sustain an idle of few hundred rpm (if and only if it's cracked enough since airflow won't windmill it any longer) but if you cut the mixture after feathering instead of before, it wouldn't necessarily have the time to foul the plugs.
In reality, of course, you could cut the mixture and have the blades spinning (windmilling) with airflow, then feather. But FSX limitation will make the engine affected stop even when a real engine wouldn't. Therefore for semi-realism, I'd prefer throttling back, feathering, then cutting the mixture. In fact, I did try cutting the mixture and feathering the prop (while flying) - no luck feathering it with prop stationary. Restarted it and feathered it with throttle cracked (mixture auto-lean): worked like a charm, rpm dropped to aroung 500, shut the fuel valve and let it drain the pipeline dry. Then 0 rpm.
Unfeathering can be done with a stationary prop since they're built with an electric oil pump for unfeathering procedure. I guess the pump is only one-way? (i.e feathering done with engine oil pressure, unfeathering done with auxiliary oil pressure).
There may be a delay between the time you hit the feather button, and the time the engine actually feathers. Also, you can only feather and unfeather once, so if you're trying to feather a second time (a-la Boeing B-29), you can't.
Feathering doesn't have much delay (at least with engine running, with engine stopped it might be impossible (talking FSX)). Unfeathering on the other hand takes quite a while because the electric oil pump used for unfeathering is of low pumping capacity. Or at least that's what I presume is why it takes so long. Perfectly understandable that the plane isn't packed with high capacity (=heavy) defeathering pumps since they're so rarely used. Feathered engines usually stay feathered because usually you have a good reason to feather them. And they don't fix themselves in mid flight.
I tried feathering and unfeathering the same engine several times. No problems repeating it with A2A B-17. Bad modeling, or is your information incorrect?