June 2016
I just encountered the same issue with my Origin copy. I have all the DLCs installed. I ran a repair on the game from within Origin (right click and Repair Game), and the issue is now resolved. This seems to indicate that the issue is with DLC install order. I hope that this helps anyone with the problem.
November 2016
Definitely still a problem. I've tried many of the solutions including doing a repair install and making sure all weapons are not marked "New" after picking up the SMG in the Mars mission. Could pick up the first two SMG mods after this, but the shotgun/sniper mods in the rest of the mission just vanish when I pick them up. Can't even buy them in the Spectre store on the Citadel because I "picked them up."
I've thought about doing a playthrough without picking up ANY mods figuring I can buy them in the store later, but apparently there's a limit to how many times you can buy the same mod in stores, which would leave me with Level 2 weapon mods. No good.
Tried the Mother of All Mods mod, which is basically a cheat mod. You can buy every mod/weapon for peanuts when you get to the Citadel for the first time. And they're not organized at all. All weapons are lumped together and mods and thrown in at the bottom. It's a mess.
March 2017
I registered just to comment on this bug. The fix the gentleman on page 2 lists is the only fix that seems to work, unless you download one of the mods that gives you all the weapons mods in one big mess. The good news for Xbox users, is that you can use a program like Horizon to transfer your Xbox save to your PC, where you can use Gibbed's Mass Effect 3 editor to Mod your save and then transfer it back to your Xbox HDD. For info on how to do this, you can search for Xbox to PC saves to learn. It's not real complicated, but it is a pain to have to go through all this. The good thing is that you will learn a valuable skill in transferring save files back and forth. I'm not sure if this works for PlayStation users, but I know there are some Youtube tutorials about PS to PC and back again, so you might have hope.
I personally think that this is a total game killing bug for people that like these types of RPGs. But I was pretty certain BioWare was not going to do anything after they announced that they were not providing controller support for the PC version, saying about their developers: "we were stretched to thin." Wow...
Anyway, its a decent fix. Thanks for your time. For purists, you know you would find all the upgrades anyway, at least this allows you to get some credit for that, in a total BS kind of way. Gibbed's save editor is not that hard to use if you follow this man's guide.
March 2017 - last edited March 2017
So doing what the guy on page 2 said. i noticed a little something in the save editor
All the mods have capital letters in SFXGameContent.
but the 3 mods that keep giving me trouble in my current game (pistol magazine, pistol piercing, rifle piercing) have lower case sfxgamecontent
I tried changing it to capital but it reverts again when i save my game.
Edit: Just completely deleted the mods from my save. then readded them made sure everything is in capital letters. load up my game. save. and it's back to lower case.
The fact that these are the only 3 mods that give me problems on every mission. my bet is that it has something to do with the capital letters. might be worth checking in coalesced.bin if the problems in there somewhere. but sadly i got no clue where to look XD
April 2017
Hi,I can confirm that this bug is definitely caused by the patch (maybe the bug was caused starting with the patch 1.03 like someone else said) and not the DLCs as i've tested when i installed the patch 1.05 i couldn't pickup the mod on Priority:Surkesh but when removed the patch while with all the DLCs intact the mod registered fine again when i picked it up so you only need to remove the patch (doable on Pc) and not the DLC.
December 2020
you know what's crazy? i FINALLY have the entire game (all the DLC, etc) installed and after 4 flawless weapon-modding adventures on my old laptop, i now apparently can't mod my weapons on my desktop computer/full Origin game. it's _7_ years, and the Legendary Edition is coming out next spring. and they NEVER released a fix for this.
W.T.H.
i have other mods installed, so i'm _loathe_ to mess with my save, but it seems like the only solution people have found so far??
October 2022
this solution worked like a charm (using the Gibbed savegame editor)
October 2022