Yes, it looks like the apha_gamma uniform is not always properly set on some shader (and then ends up at 0.0, ruining the eyes)...
To work around this issue, replace app_settings/shaders/pbr/class2/deferred/alphaF.glsl with the file in this archive:
I'll come out with a proper fix for next release.
EDIT: fix found and implemented, and it also improves eyelashes alpha (too transparent in PBR mode) when the alpha-gamma workaround is enabled.