Does PrusaSlicer 2.6.1 for MK4 have UI bugs, or am I missing something?  

For a more accurate diagnosis please supply your project as a .3mf file

Files > Save Project as

Zip the .3mf and post it here. It will contain both your part and your settings.

However, here is one possibility:  The default first layer is 0.2mm - and DO NOT change from that default without very careful calculation...

So, your second layer starts at 0.2mm, the third at 0.45mm - below the colour change setting, the fourth at 0.7mm - over 0.5mm so colour change here ...

Your changes do not match the layer heights; simplest would be to change to 0.2mm layer heights and set the change at 0.4mm - whether you continue to 0.8 or 1mm is a matter of taste.

Cheerio,

RE: Does PrusaSlicer 2.6.1 for MK4 have UI bugs, or am I missing something?

I'm pretty sure Diem is right. Unless you changed the first layer height to 0.25 as well.

RE: Does PrusaSlicer 2.6.1 for MK4 have UI bugs, or am I missing something?

Sorry, I thought I had attached it, but it wasn't zipped so it disappeared I guess.

I did change the first layer height to .25.

Modified 0.3mm draft with 0.25mm layers and 0.25 first layer ...

There's just too much mixed up; for a job this small go back to a vanilla 0.2mm profile and set the change at 0.4mm.

Or take a look at: https://forum.prusa3d.com/forum/original-prusa-xl-tool-changer-how-do-i-print-this-printing-help/printing-multicolor-flush-text/#post-681520

- where I addressed a similar problem from the other direction.

Cheerio,

RE: Does PrusaSlicer 2.6.1 for MK4 have UI bugs, or am I missing something?

Nothing wrong with your 3mf file. It's just how Prusaslicer shows you the layers. When the slider is all the way down at the bottom, it shows you the first layer on the screen, and the label says 0.25mm. Then you can move it up 3 times to see the next three layers. It's a bit confusing but you'll get used to it. 

But worse, the color change is set at the UPPER end of the layer where the change happens... So to get two layers of clear and two layers of opaque, you'll have to click on 0.75mm in the slider to set the transition (the upper end of the third layer). Again, confusing, to say the least. In your 3mf the transitions happens after the first layer.

I always double check by sliding through the layers that my color change locations are indeed set were they should be. 

RE: Does PrusaSlicer 2.6.1 for MK4 have UI bugs, or am I missing something?

Thank you! It is indeed confusing.

One more thing: I have 2 layers of type, extruded all the way through, on top of the 2 layers of clear. When I watch the animation, the top clear layer, next to the type, has the type traced into it. Experimenting with very  thin layers, this perturbation seems to extend about .05 mm into the clear layer. Why should the clear layer be disturbed by the opaque type layer above it? Is there any way to reduce this? I think it makes the clear layer less attractive.

RE: Does PrusaSlicer 2.6.1 for MK4 have UI bugs, or am I missing something?

Yeah... that is a "feature" that I wish I knew how to adjust. If you look at the preview and switch from Color Print to Feature Type in the legend, you see that PS is starting to put down solid infill in those areas that will also be covered in higher areas. In many models (say a peg sitting on a flat surface) that makes a lot of sense as it helps "bond" those features to lower levels. In your case—where you're using transparent filament—, it doesn't. I'm not aware of a way to modify this behavior in PS.

However...

You can cheat. See the attached 3mf file. I used the cut tool to cut the plaque into two objects at Z = 0.5. The problem is that in Prusaslicer you cannot lift an object off of the print surface. However, you can lift parts. So I added a small 10 x 10 x 1 cube to the opaque object with the text, aligned the text with the transparent sheet, and lifted it up so it sits on top of the other object. When you look at the feature type now, you see that it finishes the bottom object before starting the top object.

I didn't print it myself to make sure it works but hopefully this helps.