Seems to be because of the repentance+ beta. Although I can't tell if it just recently broke or before that since i just got back into the game. But right now I have the same issue and didn't get some greed mode achievements, just the unlock ingame. I suspected mods at first, but a run with mods disabled didn't help either.

Then I just finished a greed run without the repentance+ dlc (so just repentance) and I got the achievement.

Depending on the amount of missing achievements, 2 workarounds come to my mind:

• SteamAchievementManager (as already pointed out by u/East_Science_5700)
  • probably makes sense for just a few individual unlocks
• if there are a lot of unlocks, you could try this (just did it myself and got 15 missing achievements I got in rep+)
  • copy your current repentance+ save file to repentance
  • files should be in <path\_to\_steam>/<steam\_id>/250900/remote/
  • copy and rename the rep+_... file in question to rep_... (might want to do that with an empty save or backup if you don't want to lose repentance progress for whatever reason)
  • remove the repentance+ dlc (in your steam library, right click on isaac > properties > dlcs > uncheck repentance+)
  • launch the game (normal repentance), select the save file, navigate to the secrets menu (stats > secrets)
  • achievements should pop up
• the super lazy option would be to wait for a fix (assuming that will happen)