In order for the balloons to match the BOM, you have to do one of two
1-The drawing view must be of the same configuration of the same assembly
as the drawing view to which the BOM is attached.
2-Lock view focus on the drawing view to which the BOM is attached while
placing balloons on other views. You won't be able to drag a balloon from
one component to another and have the correct item number.
This IS documented in the help somewhere, I just can't remember where.
Someone please jump in if I've left something out.
Item numbers don't show properly through Broken-Out sections I have reported
this but haven't heard that is has been fixed. To work around you have to
attach to edges only and not surfaces in broken-out sections.
You could try doing this, select a view that you already ballooned. Then RMB
and go to 'Properties...' for that view. In the lower left corner, check the
box to 'Keep linked to BOM' and make sure you select the correct BOM from
the drop down list. Usually 'Bill Of Materials1'. This always fixes that
problem for me.