When I decode a PL tone from a WAV file I use audio editing software like CoolEdit (I think the free program Audacity will do this as well). I, for some reason, have never had any luck with Wintone.
And yes, the higher PL frequencies are mroe audible. A good radio will try to filter the tone out somewhat so that it can't be heard very prominently, but that only works to a certain extent. That's why I like DPL/DCS.