xfce-base/thunar-1.6.3 does not use the default applications for different file types correctly. This bug seems to have been fixed upstream, but the fix hasn't been imported to Gentoo yet. Reproducible: Always
I'm using glib 2.42.2, thunar 1.6.3 (hope will be bumped soon) and xfce 4.11 (all xfce packages testing) and I can confirm this bug. I don't know if it is related but I can't set the preferred application even with pcmanfm. For example I try to set eye of mate for png images but even if I check "use as default for this kind of file" both thunar and pcmanfm keep trying to open png images with "wine internet explorer" (I don't know why, I uninstalled wine years ago).
should be fixed in 1.6.6 according to upstream.
1.6.10 is now the stable version