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.