this mod maybe uses a questionable way to store items in the companion's inventory. the message pops up only once when added. this means your mod adds the items 10 times somewhere! if i find the time i will have a look at it...
Hm, allright, had some more experience with the event.
It seems to me that it happens during the weight measuring of the companion-chest, which is done right after closing it.
I'm guessing that the backpack deciding script is ran at the same moment?
Could it be that timing your script a second or so afterwards, might solve the prob?
Furthermore,
in interior locations the amount of message boxes is 10, in exterior 30 to 35(which is where it get's kind of annoying;p)!