we are not talking about the mission items
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I've started to note what items I see being red. First, they have always been white for me. Second, they do seem to come with a couple mod slots, but that may just be that I've reached a high enough level for that to come with most weapons. Third, I have seen a weapon that I have already picked up (so it wouldn't be that), but I did not equip it, so it could be that they mark weapons you haven't previously equipped (although that would mean every pistol should be red for me since I never equip them and I've seen plenty of pistols that aren't red).
My guess it that they could be weapons that are especially effective against the enemies in the mission, but I have no way to confirm this. This is just one of the reasons I really want a user manual for this game.
I haven't been paying enough attention to confirm for sure, but I'll third (or fourth, or whatever) the theory that it's flagging items of a type you've not previously found (edit: or sure, maybe used) before - I was getting that effect a lot more often early in the game than now, and from my admittedly hazy memory I'm pretty sure most of the more recent ones for me were launchers and stuff that I'm starting to see more variety of sub-types in (i.e. single shot guided, swarm, manual detonation cluster, etc).
Definitely doesn't seem to have anything whatsoever to do with rarity, mods, base stats, or anything of that nature.
I always thought they glowed red because they dropped because of the extra 10% loot chance you get for pre-ordering. The loot boost.
Weapons that drop that are glowing red are supposedly very rare drops. I have not gotten very good weapons out of red glowing weapon drops, but you will occasionaly get some good weapons from red glowing items.