I just had the issue of queing up for quick play Empire wars. Having hide out, Mongolia and Arena banned, Arabia preferred.
I still got a match on Arena. I checked after the match and it still was banned.
Two question for you:
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Didnt you just look at RM and sets your bans for RM? If you then click EW, then you might need to select the bans again.
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This look likes the bans for 1v1. Did you play 1v1 or did you join a team game?
It was a 1v1 and I had the maps banned specifically for Empire Wars. Yes.
I agree, @MustySnizl, this does appear to be a related issue to the issue I reported. The video recording in there may be of use to anyone wanting to verify that this is not user error.