If you've played this game at all, you've probably noticed the counters for accumulation achievements don't work. There's a lot of theories about this posted around, but they're either out of date or incorrect speculation. The most commonly thing stated, watching the credits at the end to commit the stats to steam is plausible for how it used to work, but there have been updates since then, and the credits no longer show at the end of playthroughs, which might be why it appears completely broken now. Fear not, however, as it is still possible to get these achievements if you're willing to jump through a lot of hoops.

There are 3 seperate copies of each counter:

1. Counters stored on steam. These never seem to update no matter what you do in the current release.
2. Counters stored in game memory.
3. Counters stored in the save file.

Whenever the main menu is loaded, the counters from the save file are read into the memory counters. Then the game requests the counters from steam, and if it gets them, replaces the counters in memory with the ones from steam. Whenever the game saves, the counters in memory are saved to the save file. As you play through the game, the counters in memory increase, and if they hit the unlock point, they unlock the achievement. The counters in memory and the save file are never pushed to steam.

Therefore, under normal playing conditions, every time you load the main menu the counters are all reset, since they are loaded from steam, and the steam counters never increase. However, the game will keep using the counters from the save file if it fails to read the counters from steam.

In order to prevent the game from reading the counters from steam and clobbering the ones from the save file, you need to do this procedure every time you want to start or continue a game:

1. Select a game other than Organ Trail in your steam library.
2. In the steam menu, go to Steam > Settings > Download, and click Clear Download Cache. The download cache saves local copies of many things about your account in steam. All of this will be re-downloaded automatically as needed, so don't worry about losing anything. Steam's local copy of the achievement counters it will use if it can't contact steam servers is part of the data that will be removed, which is why you need to do this.
3. Click Ok on the confirmation box, and the Steam login box will pop up shortly, so log back into Steam. Steam will remember which game you had selected in your library, and re-download the information about it's achievements immediately when you log in, but won't do the same for other games until you select them, which is why you needed to select a different game in step 1.
4. Disconnect your computer from the internet, then select Organ Trail in your library.
5. If you've done everything correctly, No Connection will show up shortly in the bottom of steam, and the information on achievements will not show up in the main window. It should look like a game that doesn't have achievements.
6. Click on play, and click run game when steam nags you about not being able to cloud sync.
7. After the main menu is loaded, you can reconnect your computer to the internet.
8. You can now play the game normally.
9. If you end up back at the main menu for any reason(won, lost, return to menu from pause menu, etc), immediately quit out of the game. If the main menu loads after you've reconnected your computer to the internet, it'll clobber the counters in memory with the stuck ones from steam. The game does not save right away though, so if you quit out without doing anything which would cause it to save, it won't clobber your counters in the save file, so if you end up back at the main menu, do not start a new game, do not continue a game, do not change the settings, just don't do anything other than quit.
10. To continue playing(start/continue a run) go back to step 1. As long as you do this procedure every time you start/continue a run, and quit out when it sends you back into the menu, your counters in your save file will continue to work properly, and the achievements that depend on them will unlock correctly. The progress on them won't show up in steam, but that doesn't matter.