Hello, HBB.
I am not quite sure which issue you are reporting.
Is the issue that
+ in your subbars the back button to Main.bar sometimes disappears?
+ in your subbars the back button to Main.bar is sometimes not displayed?
I.e. do you expect it to be always displayed or do you expect it to be always absent?
Telling from the title you expect the back button to Main.bar not to be displayed in menu view. Why? The buttons exists.
Why do you refer to the same bar-file, Main.bar, once using %COMMANDER_PATH%\..\Common\Bars\Main.bar (which is consistent with the other path specifications) and once using %COMMANDER_INI%\..\Bars\Main.bar (which makes it unnecessarily hard to verify you really are referencing the same Main.bar file)
I agree that T.C. should be consistent in menu view, too: either display the back button always or never. Yet, how should T.C. tell the back button is a back button to the main bar really? And where in the help file is it suggested that T.C. can do so? (Maybe I just missed the relevant sentence.)
Side issue
Sorry to say, but your flash file did not prove too helpful to me.

I am not quite sure whether the root cause is my Flash player (10.0.32.18 ), some misconfiguration on this particular machine or a problem caused by the internal file format of your flash file
BackButton.swf.
Anyway, the issue which I experienced when viewing it were:
+ poor screen resolution of the movie
+ as a consequence it was hard to really see the details
+ the movie made my browser(s) use an enourmous amount of RAM (300 MB, and the file has got only 2 MB)
As I said before, maybe the cause is on my side. In this case, you may simply ignore this complaint about my flash movie trouble.
<Added>
Explanation on my Side Issue:
Other users who use a weak machine and a low screen resolution may experience similar effects.
The first machine where I watched the flash file was my old notebook which has got a 14 inch screen only. Therefore the screen resolution has been set to 1024 x 768 pixels. If you watch the movie at 1024x768, you will not be able to recognize the details too well.
This morning I watched the same flash file at 1280x768 pixels, and the details could be recognized clearly.
About the memory usage:
The flash movie is a bit greedy to put it mildly. It runs in an endless loop. So far so good. After it had been watched once, it had consumed about 300 MB. After it had been watched twice, it had consumed about 600 MB. Watching it once more would not increase memory consumption.
</Added>
Kind regards,
Karl