Looking into this further I can see that there is a problem with the options being listed when viewing the orders. My apologies for the misinformation, it seems that I have the fix in effect already.
The fix involves adjusting the confirm and pp_confirm pages. In the store order details server behaviors in these pages the item name field must be updated. I'm including the updated versions of these pages for you. Make sure to backup your current pages before making use of the new ones, but they should allow the options to show in the orders area.
It will not update any existing orders though, only new orders will have the options listed.