Might want to take a look at the weights for the each of the variants to make sure they are set properly (a default weight is used (specified via appconfig parameter) if the weight is invalid), and also review the Is Ship Separately setting for each. If items are marked as ship-separately items they will be sent over to the carrier as individual shipments and dimensions AND weight will be used to calculate the shipping rate for that single item. Then that rate will be added to the rate of any other ship separately items before finally being added to the rate of the items that are shipping together.
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