Yesterday, Thissler and I sat down, and tested a mutual theory. (I'm naming it after Thissler of course.

as thiss was the victim of it more than I was when we played with sivar previously!) The theory was, it was Disables causing the weapon lockouts.
This theory seems to have panned out, and would also explain quite a lot of times when it used to occur in the past as well. We tested, the following, PSW1, 2 and 3, and Tricobalt weapons.
This is Thisslers video on the subject.
http://www.youtube.com/watch?v=nYZ9osym8zc
My Vid on the subject.
http://www.youtube.com/watch?v=9Mv0G...ature=youtu.be
As you can pretty clearly see, there is no AMS, and no scramble on the map here.
Something to note here, is PSW1 seems to be doing this the most frequently out of the three shockwaves, shockwave 3 seems to knock out the most weapons at once, most frequently.
We eliminated every variable, by pouring through previous footage and this was the only constant, so this is what we tested. It is
not (at least not this particular bug) AMS or scramble. It does make sense however for there to be confusion on this, as ships packing scramble also tend to be carrying a PSW1 or 3. Or for it to pop up in subsequent matches, as PSW1 is one of the most reliable methods for disabling extend shields.
The reason we suspect tricobalt does not perform this as reliably (as we could not catch it on camera) is it's stun duration is much shorter, thus the odds of it catching a weapon mid cycle are much lower. This weapon lockout seems to occur, during mid firing animation, or just at the start of the cycle. (most commonly mid point)
Do other disables knock out weapons? I do not know yet. As we did not have the resources to test them all.
I do have more videos of getting PSW to do this, as if the 12 minutes of watching my guns fall silent one by one was not enough already.
Given that this happens in Fleet Events occasionally, that is also unsurprising given the use of shockwave torpedoes by various NPCs, shockwaves by romulan warbirds, which also convers the Vault and all of the reman missions come to think of it, several pve missions as well.
Does this happen in matches with no PSW torps, PSWs, or trics? We simply do not know. This however is by far the most reliably method of capping it on camera that I have seen to date. Perhaps when computer frame rate drops, or during lag spikes you can also catch a weapon mid cycle and cause a lockout, but such a thing is pure speculation on my part, and would be nigh impossible to reliably reproduce (as you can see it was hard enough reproducing this, which is why there is 12 minutes of footage here, and almost 20 minutes of other video footage, during our testing that I have not yet uploaded) you have to catch the weapon cycle just right for this to happen.
This can also cause abilities on your power to tray to white box as well such as Distribute Shields, and bridge officer abilities. I have a second video showing this as well. In the case of abilities on your tray, this only triggers when the ability is started it's initial activation when the box is white, and you have to be stunned during that time to get it to occur most reliably. Distribute shields is the most common because this ability is activated most frequently on the power tray. Other abilities have longer durations, and cool downs so it is less likely they will be caught, but it can happen to them as well.
I have lots more footage of this happening, and even managed to catch distribute shields being locked out on film as well. If need be I can make more movies demonstrating how easy this is to replicate. Do note, this video is 12 minutes long, so you have to be fairly consistent at bumping the buttons over and over again to get it. It does not happen every time psw is hit, though by the end of our last test Thissler and I were able to consistently knock each other's guns silent, by utilizing buff and debuffs as well. (Sub nuc seems most effective here as it lengthens the CD cycle for -everything- including activation, and weapon cycles. Which gives the PSW more time to knock things out)