Emulator

I happen to own the Prima guide to the game (but I only own the game itself for Xbox 360), so here's a list of these glyph puzzles that I spotted while skimming through it:

• 1-1: The Lost Temple: freeplay only, near the end of the 5th area (the one after the idol chamber), at the end of the lower trail.
• 1-2: Into the Mountains, freeplay only, near the exit of area 4 (cavern chamber)
• 1-3: Motorcycle escape (is this the correct title? it's also used by 3-3), freeplay only, near the end of the level (blocking the entrance to the cantina)
• 1-4: The well of souls, in Area 2 as part of normal story gameplay (and in a few other places in the level too, one of which the guide claims is freeplay only)
• 1-5: Pursuing the ark, freeplay only, near the upper-left of the dig site (the first area), requires explosives
• 1-6: Opening the ark, freeplay only, hidden behind the parked truck that you repair in the second area, and a second one on the wall near the ark in the final area
• 2-1: Shanghai showdown, freeplay only, on the far-right corner of the streets area, requires explosives
• 2-2: Pankot Secrets, part of normal story outside of Indy's bedroom after pushing a potted plant
• 2-3: The Temple of Doom, freeplay only, far right of sacrificial pit area, requires mechanical ability
• 2-5: Escape the Mines, freeplay only, on the left wall of the starting area
• 2-6: Battle on the Bridge, in the 3rd area, freeplay only, on the wall near the spike pits
• 3-1: The hunt for Sir Richard, part of normal story, to enter the library and then again within the library and in the tomb
• 3-2: Castle rescue, part of normal story, several times in the study and then in the final room (you need to bring a bazooka to explode a silver cabinet)
• 3-4: Trouble in the sky, in the 3rd area (countryside), up the hill
• 3-5: Desert ambush, freeplay only, in the starting area after breaking some barrels to make a ladder up the cliff
• 3-6: Temple of the grail, throughout the level as part of the story

As for the issue itself, it looks like this is similar to the super mario sunshine debug cube issue. The highlight effect is objects 50-52 in the first frame of that fifolog, and they configure configure blending to use the output alpha, but they never actually set where alpha comes from; it's only set in object 1, where it uses the vertex color. But object 50 doesn't include colors in its vertices. Object 48 (the table) does, though, including providing an alpha value of 130 (stored as 32/64 in an RGBA6666 format). We do have a hack to adjust the value used in this debug cube case (MissingColorValue under [Hacks] in GFX.ini), and setting that to 0xFFFFFF40 instead of 0xFFFFFFFF gives something OK-looking (but I'm not sure if that's the right number to use).

If you could record fifologs of a few other glpyh puzzles, that'd be helpful for comparison. Level 3-1 in particular should be fairly easy to access (it's unlocked after completing 1-1).

https://github.com/dolphin-emu/dolphin/pull/10937 should solve this via gameini using the same hack as the debug cubes in Super Mario Sunshine.

One other thing: Does the fade in/out animation where it shows you the intended order for the puzzle work properly? Or is that also affected? (I'd assume that since that one fades in and out, it must be supplying an alpha value, but I can't know for sure.)

MissingColorValue has been set via gameini starting in 5.0-17091; please check if this fixes the puzzles completely.