Let's say theres a setup of three maps. If I go through map 1 to map 2, there is no problem. But if I try to get from map 2 to map 3 after that the trigger does not do anything. Yet, if I load into map 2 via the console, the trigger into map 3 works as it should. The trigger also functions if I load a save in map 2. Any ideas?

I've seen this problem before, and it's usually a case that the trigger positions between the two maps are too close together. You say you can transition from map1 to map2, but can you then go back? I would expect you cannot.

Basically, if you pass through a trigger_changelevel and you are in contact with another trigger_changelevel, it will be deactivated to prevent an infinite loop of going between levels. You want to set it up so that the trigger to return to the previous level is a few distances behind the player.

map1

The player hits the trigger_changelevel and loads map2

map2 (broken)

The player loads into map2, but the trigger_changelevel is in the same place, so they touch it immediately and would return to map1. This would in turn have them touching the trigger to go to map2 again and so we have a potential infinite loop. The game code prevents this and disables all trigger_changelevels.

map2 (fixed)

The player loads into map2 where they hit the trigger in map1 and can continue forward without hitting the trigger again. The transition back to map1 is further behind them, to ensure they're not running into it immediately and looping between map1 and map2