I am also having some problems with this that sound like they may be related to your "solution" posted above.
When my plugin runs, I get the coordinates for the page rectangle in the document.
Next, I get the ruler origin.
I then compare the two values (after converting them to the same system) to see if the origin is in the lower left of the page.
This all works under most circumstances. On some of my files however, after running the plug in, it correctly tells me the origin is NOT in the lower left. I then drag the origin to the lower left and run the plugin again. This time, it incorrectly tells me the origin is not in the lower left. Going through the debugger, I have determined that it seems like the page coordinates are not getting properly updated after an origin move.
If I draw some art and run the plugin again, the coordinates are updated and the plugin runs correctly.
Is there some way to force Illustrator to update these coordinates via the SDK? As I said, on most of my files it works correctly, the coordinates update when the origin is moved. But on a select few, they don't seem to update automatically.
So, after looking into it a little more, the problem seems to be related to crop areas updating inconsistently. If I have several crop areas in a document, the coordinates of the currently selected one is updated and the crop area remains positioned correctly. All the other crop areas coordinates don't change, so their positions "move" so they are in the same place relative to the origin. This doesn't seem like the intended behavior of crop areas when the origin moves.