This is not because you post Ship and Invoice in the same or different time. This is because you probably post separately purchase document. Probably, you post first Receive with cost of 1.000 and after that you post Invoice of 1.100. Because of that, you have more than one value entry.
In first entry you have receipment cost and in third entry you have difference after invoice (1100-1000). I'm not sure what is second line (in your table, value is zero). But if you use Additional Reporting Currency, this entry is here probably because difference in ACY currency cost.
Look at this (second) entry in Cost Amount (Actual) (ACY) field. If you have some value here, this is reason.