i am pretty sure, that all games count, and just the position was taken as a endresult where he plays most. So the problem i see with your player is more that he missed 3 games, and that you have a lower visiting fanbase then other teams in your league through your small arena(it is a popularity vote).
And yes the votes are often ehm curious.
I've seen numerous times cases where a player playing different positions is underrated by the ASG votes.
As for my player, he missed two games, the back-up missed one, but still:
Marcin Żurkiewicz 79160 (starter)
Francisco Ibarrola 38011 (back up)
Aurélien Novais 16426
Ballago Diarra 7074 (my player)
there's too much of a difference to be just those two games missed.