Ok, thanks for the info as I was unaware that some quests offer affection to only some companions.
Its all about the responses, your companions all have different personalities and different responses gain or lose affection with them (my agent for example runs around with ensign temple, but pulls out SCORPIO for conversations where I'm gonna be killing or generally being an arse lol)
His point was that the amount of affection gained by a positive reaction from a companion varies depending on when the companion was acquired. The later you got your companion the less of a gain you get from both gifts and conversations as you have had longer to gain it.
Taking my agent again as an example
Kaliyo +15 or -1 as reactions
Vector +32 or -2 as reactions
Lokin is i think 41 or so for positive... have to check that
Temple is 55 or -3
SCORPIO is 102 or -4
So the 400ish vs 90 may just be the fact that you are using your first companion gained vs using your last companion gained