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Oh well, oh well...
After trying a few other things, i was able to figure out that what was the problem: the XML import preferences has to be set at document level, not application level!
I suppose that the logic behind this is application level= interaction with UI and document level= interaction with script.. but it's kind of weird to save application state preference at document level and surely havent seen any documentation on that behavior.
Anyway.. Let's move on!
If you can see the behavior in the user interface, you can see it in scripting. I think it makes perfect sense to have the XML import preferences set at the document level, because some documents need one set of preferences; other documents need another. I think (hope) that the user documentation covers the differences between application and document preferences (if not, I do, in my book).
If you see a preferences object on both the application and the document, assume you want to use the document preferences. Unless you're trying to set preferences for new documents.
If you would have two different script acting on the same documents but with different settings (ex. one would append sections and the other update the complete data)... wouldnt it be dangererous to rely on the document recorded xml import preferences??? You have use case where you rely on this??
ps: It's really just to discuss as my "batch" works 100% fine now!