It seems weird I’ve not run across this until just recently. Illustrator is not identifying tints in the color palette. I could have sworn when you clicked on a shape that had a tint of a Pantone (not a transparency,) it would show as selected in the swatch palette. Nope. Maybe I’m wrong and it never did with tints.
Weirdly too, if I selected a shape with an 80% tint Pantone color, then made another shape and selected a different Pantone from the Swatch palette, it applied the 80% tint to it as well. I had to go change it in the Color palette. Yes I dumped my prefs. Still happened.
What I didn’t check, and will tomorrow was if it worked correctly with the Application Frame turned on. There’s been a whole series of glitches across InD, Illy and Photoshop regarding that. I can’t work with the application frame turned on. When I close or minimize a file I NEED to see the desktop or a file open behind it. I might have 3 or 4 projects open in those three softwares and have to switch back and forth quite often.
On another job just recently, I told Illustrator to add all used colors to the swatch palette. It failed to identify a 70-70-70-100 rich black as even being in the file. Ink limit in the rip didn’t catch it either. I don’t see dot gain often, but that sure closed up the 16pt drop-thru white text to nothingness. Had to reprint the job after going in and direct-selecting it with the Color palette open and changing it, not the swatch palette. Something seriously wrong on that one.