The reason that this is the case, as I recall, is based on mob elemental resistances. Since they no longer determine their ability to resist Skillchains in the old-fashioned way (50%, 25% etc resists) now they are used to determine damage. A mob with a higher resistance to a skillchain element will take reduced elemental damage, while a mob that is weak to that element will take boosted damage. I believe there was some review of this on BG somewhere, but I'd have to dig it up...

Either way, this may be the cause for the difference; do you remember what mobs the SCs varied on, and if it was consistent?

Edit: Found a little extra information and it is tied to species rather than straight-up elemental resistance, so threnodies and such won't buff your SC damage.