January 2013 - last edited January 2013
The last two missions I've gone on (Priority: Rannoch and N7: Fuel Reactors), I've had to completely rebuild Shepard's weapon selection from the default (unmodified M-3 Predator pistol and nothing else). This is really annoying, though fortunately I haven't needed to reapply the mods to the weapons I actually use.
PC version, N7 Digital Deluxe with all DLC.
I've noticed my weapons always reset after "Rannoch: Geth Fighter Squadrons", it probably has something to do with the weapon swap required for the quest.