Main problem is that they block light, but I can workaround it in some way.
Worse things are such strange "shadows".
They are seem to appear also near NULL-textured brushes (NULL not visible in game, covered with func_walls, but such stains stay).

I tried Zoners' newest and also Cageys version of compiling tools, same effect.

make ur func_illusionarys "normal" instead of "opaic" (sp?)(O-pay-ic)

Thanks, after some more digging I found it by myself. :)
BTW, instead of no-opaque it look better with opaque=on and custom shadow.