ToME: the Tales of Maj'Eyal

Yep. I went up a set of stairs in amon sul while blinded. After the blindness wore off, certain enemies were "invisible" - I couldn't see them, but there was a red box-target on them anyway.
I don't know about the other enemies, but the molds always were under this effect - maybe it has something to do with moving?

Yup. Just opened a door with an invisible enemy behind it... it moved towards me and ended up being a J.
Mind, I could still "l"ook at them to see what enemy they were, but the letter didn't show.

I have noticed this also, frequently, in the sandworm lair - and it's not just going up and down stairs, it's whenever you recover from being blinded. Destealthing rogues also often show up as lookable empty red boxes.

SVN 1893: rouges and sand-worm lair reproducible.

and another odd one - stealthed rogue shows up as blank square to the Cursed's telepathy power.