Tinkering around with JUCE and noticed the exact opposite problem when building a trivial sample plugin created via Introjucer. AU and VST work fine, but VST3 comes up as mono in REAPER (v5.1) and only plays the left channel. Doesn't matter whether I set the preferred buses as {1, 1}, {2, 2} or {2, 2}, {1, 1}. using latest commit as of yesterday (3 Dec 15).
Using the test host and explicitly wiring the inputs and outputs works as expected.
Also, using Cubase 7.4 works as expected.
I'll also contact the folks at Cockos.