On your examples, are you clearing off other containers to show the skulls better? I ask because the iron is high which tells me perhaps you were churning hunters each time. Isn't that what you mean by mat run?
Also, I think there's something to getting multiple skulls per manifest that ups the ratio odds. 4 or 5 at one time as opposed to 4 or 5 over a half hours time. There just has to be something different about the parameters with sailing loot. It's like taking out 3 or 4 bosses at one time.
Plus I figured you may have been talking about sailing as well.