Are the missing option values using "Variations that tell more..." showing up in your E-junkie Transaction Log? If so, we're definitely passing those along to your Integration URL(s) -- account-wide Common Notification URL, or product-specific Payment Variable Information URL when that item is purchased -- so any problem with those would be at your fulfillment house's receiving end.
If the problem pertains to option values using "Variants having individual price/weight/stock/SKU", note those are distinct from Variations and thus are not passed using on#/os# pairs as Variations and PayPal IPN would do. Instead, we transmit the 'sku' value of the particular Variant ordered -- taken from the first position of that Variant's line in your product's Define Variants configuration -- and since 'sku' is an Item Specific Non-IPN variable (documented as such on our Integration help page), it only gets transmitted to that product's Payment Variable Information URL when that item is purchased, not to a Common Notification URL.
This means if you need to transmit Variant 'sku' values to your fulfillment house, you should specify a Payment Variable Information URL for each of your products, rather than using the Common Notification URL. Each item ordered would then send its URL a complete copy of the full order data (so multi-item orders would transmit multiple copies of the order data), plus some Item Specific Non-IPN variables to help identify which particular item in that order triggered any given transmission -- see the section on Item Specific Non-IPN Data here for documentation of those variables:
http://www.e-junkie.com/ej/help.integration.htm#data
E.g., if your Payment Variable Information URL receives a submission with item_cart_position=2, that indicates that submission was sent for the item identified by 'item_number2', 'item_name2', etc., so the 'sku' value in that submission would go with that item. Another approach you could take is to make sure all Variant 'sku' values are unique even across different products, so any 'sku' value received could only ever match one item anyway.
