I don't think there is any common mistake in using the document architecture 
that would cause the weird problem you describe.  Therefore…

On 2011 Jan 10, at 19:01, Shane wrote:

> when I … run operations from the main menu or the toolbar

To debug complicated problems, it is usually best, if you can, to ignore the 
forest and focus on a tree; that is, focus yourself on *one* simple, 
reproducible test case.  If you find the beetle that is eating this one tree, 
the other trees probably have the same pest.

In this case, that means to forget about "operations" and pick *one* operation, 
preferably the simplest one, which is misbehaving.  Study what should happen, 
step by step, and debug to see what is actually happening.

If you can't find the problem after doing that, re-post here, explaining what 
you found in studying this *one* "operation".

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