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There was a fix for something like that in one of 6.1 releases - are you using the latest version?
See 6.1.5 release notes for more info: http://www.tableausoftware.com/support/releases
Corrected a case where quick filters would erroneously display horizontally rather than vertically, causing scroll bars to appear.
I think that is the answer. I'm running 6.1.2. Thanks!