It's a known issue. Here's an explanation from someone far more tech savvy than me:
Xoisite wrote...
This has now happened to me three times, and so I decided to do a little investigating.
The issue seems to be that ME3 is, at random, replacing the .gpd file in your gamer profile with a fresh copy.
For those who don't know, every game you play adds a .gpd file to your gamer profile. That is why it gets larger as you play more games. This file can contain many things, such as preferences, what missions you have unlocked, etc. But it always contains the text and icons for achievements.
When the file is reset for ME3, your currently unlocked achievements, which are stored in a separate file, are preserved, but any progress you have made towards other achievements, along with all bonus powers that you have unlocked, are reset, as that data is stored solely in the .gpd file. That file also stores things like your control settings, which is why those are going back to default.
I suspect that this issue has something to do with the process of connecting to the EA servers. The login info for your EA account is also stored in the .gpd file, and it is accessed immediately when the game starts up. (side note: anyone notice how long it takes to log in to those servers? Compare that to ME2, which also connects to EA servers at launch....)
Let's just hope they really are aware of this and can patch it, otherwise I'll never get some of these achievements... For now, I have disabled to option to auto connect to the EA servers. Since doing that, I have not had any issues.
Disable your automatic login to EA servers. That has worked for me. For now,