It doesn't happen in just VS, though that is where I see it more. I've left a Civil War with 100 WZ comms, but had maxed the amount of medals(8) to get rewards for. Same as Huttball and Novare coast, though those two range from 100 to 130. And no, these weren't only after dauntless medals were rewarded, in quite a few of the cases I'd already had 8 medals before the dauntless medals were rewarded, or there weren't any dauntless medals at all. I've left a loss with 80+ WZ comms. before, and had wins(especially VS) with the same amount. Before this issue, if I maxed medals reward, I was leaving WZ wins with 140+ WZ comms, and losses with 80+.
I THINK you are right. I took some screenshots a week ago of some sub-50 Huttball I believe where it shows me getting more with a loss that it does a win with more medals. Will have to try to remember to look when I get home from work tonight.