I recently acquired the Altar of Despair expansion.

From reading the rules PDF in advance, I had the impression that heroes would not know whether a particular glyph of transport was a normal or dark glyph until after activating it. However, the dark glyph tokens I received have a noticeably different coloration on the back (unactivated) side than normal glyphs, making it fairly easy for an observant hero to tell that it's a dark glyph (though not which kind) as soon as it's placed on the board.

Is this intentional, or a misprint?

I'll have to check mine when I get home but I am pretty sure the unactivated side on mind look the same as the standard glyphs.

misprint

the first printing of Altar of Despair came with the cardboard in these resealable bags and had significantly better quality cardboard than the subsequent reprints of Well of Darkness (and, I'm assuming, the reprint of AoD). When I got my copy of Well of Darkness, I was really disappointed...

Anyways, my dark glyphs are slightly off color from the regular glyphs, but you have to compare them side by side to see it (unless you're some kind of perfect hue recognition person). I know my prolonged action order tokens are obviously the wrong color (blue instead of royal blue of the original order tokens), so there's a good chance the colors simply aren't consistent in either the proofs or the manufacturing.

I should probably mention that the two regular glyph tokens included in my AoD set are indistinguishable (to my eye) from the tokens I already had; only the dark glyphs look different (more yellowish).

Sounds like a color design mistake. You may be the first to notice, hahaha

I checked mine and they are slightly different colors. I don't think anyone would notice unless they were looking for it so mine might not be as bad as yours. You could always just mark the white side of a normal glyph indicating it's a dark glyph and then swap them out when activated. I know I have way more glyphs than I need.

Mine are slightly discoloured, but I have a couple of regular glyphs which have the same discolouration (which I assumed also came with AoD, although perhaps it was WoD). Either way, I make a point of including the discoloured regular glyphs as often as possible which actually makes my sharper players think they're Dark. Sometimes they are, mostly they're not.

If you're concerned, use the glyph tokens as placecards, then come up with a way to randomly determine the type when they get to it (i.e. put the glyph marker in a cup with the rest and draw randomly)

Disappointing to hear that this happened, but slight colour shifts like this are almost impossible to avoid in the printing industry (as my brother would be able to tell you in more detail) I had a related problem with a couple of the expansions for Arkham horror... Some of the cards were a slightly different size; not enough to notice unless you're squinting, but enough that cards from the same expansion tend to clump together.

The dark glyph tokens for my game came out wrong also. I get around this by buying and holding the cursed glyphs in my stack of counters. I put a normal glyph out, make a note which type it is and when the hero's flip it tell them that it is actually a cursed glyph. Because I bought all the glyphs at the start of the game and they no this there isn't any problems.

Brian