Lionel smoke whistle issue

A couple of queries: (1) how new is this engine and (2) what's the actual volume of smoke being output from the whistle aperture per chuff? I assume it's more than a trace but a lot less than the main stack volume. 

I mention these points because after having 4 Legacy engines with the dual chamber/resistor configuration, I have always seen a certain amount of "bleed" between the smoke outputs, but especially when the engine is new and the batting has not had much use. With time it reduces for some reason although I can still see the main stack smoke seem to increase slightly when the whistle is activated.

It's a bit more of a puzzle in your case than mine because on yours the whistle smoke output is separated from the smoke unit by a long tube. Nonetheless, the smoke funnel for the two outputs shows that they are practically next door to each other so some bleed between them seems inevitable:

The engine I have that most shows the same effect is a Legacy AC-12 where the smoke funnel looks like this (the smoke unit looks the same as yours):

After a lot of observation, I can't see that this is a programming code issue or otherwise the result of one fan (on the whistle side) running when it should not. I understand that there is always heat in the smoke chamber for the whistle in these units so that there is output immediately you trigger the whistle. With that kind of arrangement there will always be some quantity of smoke vapor on the whistle side and it's to be expected it will get into the adjoining funnel. 

While I do not have this engine so am guessing on this, my s-3 did same thing after I changed out smoke batting I accidentally put the metal plate in upside down this plate divides smoke stack from cylinder smoke so with plate with the recess at the top it allowed smoke to come from both sides of smoke unit the recess must be at bottom of smoke unit this allows smoke fluid to seep from main fill area into cylinder smoke unit chamber yours would be for smoke whistle.

see if yours has the divider with small recessed area at top flip it and poof issue all gone also make sure batting doesn't allow smoke to get past recess at bottom of smoke Chambers hope this cures your issue.

Now if top of smoke unit isn't flat to where gasket not sealing between smoke chambers you can use automotive high heat silicone sealant it will cure that issue it works I used it on the s-3 to date no fires etc and top is sealed between smoke chambers and pcb board yet allows to be disassembled it's not permanent as you can remove it from all parts, word of caution make sure fan motor impellers don't get silicone on them it will stop fan rotation in it's tracks.

One wonders if the plugs are reversed on the RCMC and the whistle smoke is connected to the stack and vice-versa?

Thanks for the feedback all.

i will take it apart tomorrow and operate it with the lid off to see if any of the plugs might have gotten swapped

the metal divider is positioned with the gap on the bottom of the bowl.

i’ll also check the separator funnel to see if it it fitting tight to the top edge of the bowl and gasket.

Just an update on this:

Opened the unit and ran it with the cover off. The smoke unit's fans appear to be working correctly.

The removable divider wall is also positioned correctly with the gap along the bottom.

The culprit may be the lid of the smoke unit (the board as well as the manifold that directs the smoke). They both seem to be warped slightly and bowed upward in the middle and that is probably allowing smoke to pass over the divider wall and seep from one source to the other.