This is going to be a short and simple complaint:

The following Steam Achievements show as locked for my level 30 lockpick/hacker/gun nut/diplomat:

Up and Comer (Reach Level 20)
The Boss (Reach Level 30)
Hack the Mojave (Hack 25 terminals)

I should have all three of these, but likely don't because of one simple fact: The Console (~ key). If you use it, you seem to lose access to Achievements for that game session. Considering I sometimes play for hours at a time and constantly have to use the console to fix problems with the game that cannot be fixed any other way,, I find this to be absolutely ridiculous. I am being punished because the only way I can get past game bugs is to use the console? I can't count the number of times I've had to turn clipping on to get unstuck, or have had to give myself items that were supposed to be given to me in quests but weren't (Pimp Boy 3 Billion comes to mine).

If you're going to lock out Achievements when people use the console, then make sure your game works properly first.

When you need to use the Console to fix issues quicksave and quit to desktop. Then restart the game.

...or is that too much trouble?

Nope. That's what I'm going to have to do from now on. The problem is, nowhere are you told that this is the case, except for in the support FAQ. If they're going to do this, there should be some sort of warning.