Vlad, sorry for delay, I'm having many graphic problems with the latest 2017 patch, I think I'd better do a re-install.
Anyway, I've attached a simple .tcw file, it has two objects with materials that only differ in the material name. As shown in the attached gif animation, the one on the right animates correctly because I added a second command, (PenColorInc in this case), with the one on the left, after animation and in the object properties it shows the transparency script has completed correctly but its not displayed on screen correctly.
A second problem since installing the latest patch (build 38.2) is that objects with a default material name (example plain blue) do not show the animation at all, neither on screen nor in properties, as can be seen if the material of one of the spheres is change to just plain blue, and the animation is re-run, hence why I had to rename the materials to plain blue copy and plain blue copy2.
All that said, the fact I have now got other problems with 2017, it may be something on my system which is interfering with TC.