Item Numbers in Balloons not matching BOM

Hello all. I'm using SolidWorks BOM's for the first time (on a drawing) and am having some difficulties.

I put a view of an assembly on the drawing, then inserted a BOM based on that view. All is well.

I then inserted an exploded view (created from a different SolidWorks configuration) and added a few item bubbles, however the Item Numbers in the bubbles did not correspond to the correct Item Numbers in the BOM. Item 1 was the same and that was it.

Now - it is a complicated assembly and contains several SolidWorks configurations for exploded views. The view the BOM was created from had everything visible, where as the exploded view I was annotating had 80% of the components of the assembly hidden (not suppressed). Not sure if this relates however it's the only reason I can see for Item Numbers not being the same.

How does one get consistent Item Numbers across multiple configurations (assuming that's my problem)?

By the way - we're currently using SW 2011.

SolidworksBill Of Materials