I have the same bug. None of my pillars glow to indicate the hour. And none of them fill up to indicate minutes. The spinning still works however.
I watched the preview video and it seems to be working whenever that was recorded

I went to the git-hub and tried out a few different past versions of the wallpaper to see when the bug was introduced, however the glowing feature did not work on any of them. Maybe it is something to do with my computer or my version of Wallpaper Engine.
Its a shame because everything else on the wallpaper works perfectly!

Maybe the author modified an option that wasn't intentional.

It isn't working for me either, but i noticed that it was never completely correct anyways, because on the OG ps2 the pillar would be filled at the start of the hour and drain over 60 minutes, rather than fill over 60 minutes. The orbs also don't slowly space out in diameter over the course of the hour, and the orbs also don't meet at where the hour hand's location on the clock would be at the start of a new minute. I'm not sure if these are all bugs or just oversights.

I bought Wallpaper Engine just for this clock, since I really love the PS2 clock, it would be great if they implemented the feature that the pillar fills up as time goes by or added something similar like a little ball or a square or something that shows that the pillar is filling up, which is the feature of this clock, please developer add this feature, thanks for thinking of retro gamers.

I'm looking in the "presets" section and I see that there are people who have contributed presets with the pillar clock working, if any of you happen to read this could you post what version of wallpaper engine you used and what version of the playstation 2 clock you used? Also, if you could post what graphics card you use, thanks.

I have discovered the problem, the problem lies in the Wallpaper Engine itself. The clock pillar will work until version 2.2.8, but in the latest version 2.6 it will not work. It is a shame that I have to resort to older versions to have a fully functional product, and even more so that the team has not given me an answer here.

I thank the author of this watch for correcting the pillar, or prism as mentioned in the update, with this I am calm and all of us who like this watch, just a tip or a suggestion, add an option to make the prism look brighter or less bright in WE, since in my opinion it looks a little pale unlike the original, anyway thanks OMGparticles.

The author fixed it.

Thank you so much Author for fixing this!!!