could it be that whatever theme you use provides
for its own toolbar-sections, thus circumventing the general shadow
tiddler called ToolbarCommands?

I'm afraid not - there's no theme involved.
The issue be reproduced in a vanilla TiddlyWiki by executing the following lines after startup (e.g. from Firebug):
    config.shadowTiddlers.ToolbarCommands =
        config.shadowTiddlers.ToolbarCommands.
        replace("+editTiddler", "").
        replace("+saveTiddler", "");

When (re)opening a tiddler afterwards, I would expect the save/edit commands to have disappeared - but that's not the case.

B) On the other hand doesn't the core provide some theme-switiching
capability via story.switchTheme() so you could call a refresh on the
current theme?

I've tried that (along with various other refresh functions) - no joy.

C) What's the purpose of loadShadowTiddlers and would that somehow
play a role in your refresh problems?

loadShadowTiddlers only populates config.shadowTiddlers, doesn't it?

D) Finally, I hope I am not getting off-topic here, but how would...
jQuery().trigger("loadShadows");
...in function main() do anything? I can't find "loadShadows" being
attached anywhere.

http://trac.tiddlywiki.org/ticket/1228

I just watched...
http://www.youtube.com/watch?v=WzHRHLd7tyk
...and something rather curious happens from 6:30 up until 7:10.

I'm not quite following - but I reckon the issue there is related to TiddlyWeb permissions.

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