Mass Effect 2 LE Achievements Unlocking in Steam but Not in Game

I'm having random achievements not properly unlock when playing Mass Effect 2 (Legendary Edition) on my PC via Steam. All achievements are unlocking in Steam, but in the game itself, the affected badges are dark, even when a counter shows the proper number. For example:

• Tactician 20/20 (not unlocked)
• Warp Specialist 25/25 (not unlocked)
• Doppelganger: Help the Justicar resolve her mission (mission completed; squadmate shows as loyal)

Loyalty missions not triggering the achievements also means I can't assign their respective bonus powers to Shepard. I also don't know what it will mean for the Suicide Mission at the end of the game—though squadmates with completed missions are showing as loyal in the team inspection view.

This may be related to the known (and fixed) issue where all achievements would disappear on XBox saves, but it only affects some achievements, and seemingly without any particular pattern. This solution might work, but I'd prefer to avoid it if possible, since it seems to wipe achievement progress and the OP never reported back to say if they were able to get the achievement after resetting their progress on it.

EDITED TO ADD:

After looking into this further, I realized that the same achievements that are dark in-game are missing in Origin, and the missing achievements are sequential. Steam shows 62 achievements, including, in reverse order:

Today (3/16):

• Doppelganger
• Ghost Ship
• Warp Specialist
• Tactician

Yesterday (3/15):

• The Justicar
• The Assassin
• The Quarian
• Colony Defense

Origin shows 58 achievements, most recently:

• The Justicar
• The Assassin
• The Quarian
• Colony Defense

So, presumably something happened between yesterday and today that started blocking achievements.

I did delete igo64.dll to prevent Origin in-game from showing up even though it's supposedly disabled both globally and for MELE, but I believe the recycle bin showed I deleted it on the 14th, so if that was the issue, it should also have affected my achievements on the 15th, which obviously it didn't. I'd also previously deleted the same file, I believe when working on ME1LE, and it didn't block any achievements then. Nevertheless, I have restored the file and restarted Origin, so we'll see if that does anything.

After restoring the file and restarting my computer for good measure, I loaded a save from just before the last phase of Samara's loyalty mission. When the mission finished, the achievement unlocked in Origin, but it did not unlock in the game. Even talking to the character on the Normandy post-mission did not cause the in-game achievement to activate or make her bonus power available to Shepard.