http://bugs.winehq.org/show_bug.cgi?id=6233
--- Comment #11 from Frédéric Delanoy frederic.delanoy@gmail.com --- (In reply to Rosanne DiMesio from comment #10)
As is, it looks like only the "windows version" is selectable for each application IMHO.
In the six years I've been on the forum, no one has ever expressed confusion about it.
That might be because people just don't know about this (it is not mentioned in the FAQ) and just stick to one wineprefix per application. I was confused about it, as did the OP.
However, explanation from comment 1 still holds. The fact one has to say "This tab is linked ..." is a sign that the UI isn't as straightforward/self-explanatory as it should be IMHO.