I had the same problem too on my Recon ship, and in addition to the graphical weirdness, it actually also caused one front facing weapon to become completely inactive. I tried swapping dual beams, beam arrays and torps, to no avail.
I also shared a feature in common with your setup, Ashcraft - and it turns out to be the key feature that unlocks this mystery...I too had NO MISSION POD.
After chatting to a guildmate who also has a Recon ship, I suspected it might be the Mission Pod to blame so I went to Spacedock and refitted my ship to include a Mission Pod. It wasn't as easy as you'd think though...you can't simply reselect Mission Pod once you've taken it off because the selection option disappears when you select None. Instead you have to keep hitting Randomize until it throws up a configuration with Mission Pod included.
Bizarrely though, there was an upside here - I wasn't charged a penny for any ship alterations. Not sure if that was a bug or something to do with the fact the Mission Pod selection system is borked, but the fact remains, that customisation session was free.
Anyway, when I tested the ship, as I'd suspected the Dual Beams were now originating from the Mission Pod rather than behind the left nacelle, and my weapons were no longer mysteriously becoming inactive.
Evidently the customisation options for the ship to have no Mission Pod is at the heart of the misplaced beam, so until the devs fix that, seems we have to have a Pod for the sake of functionality whether we want one or not.
I fly an RSV with no mission pod also, how can you tell one of your front weapons isn't working?
Well, in my case, I stopped seeing (and hearing) the dual beam, its icon in my power tray became greyed out, but most of all I noticed enemies were only taking half as much as damage. Weapon swapping and application of Engineering skills had no effect, and the weapons remained inactive until I zoned.
Bizarrely, this same weapon malfunction issue has become to afflict me again, SINCE I refitted my Recon ship to have a Mission Pod once more. I've submitted a ticket on the issue.
I suspect the Mission Pod will turn out to be the cause of these misalignment and malfunction issues - I've not seen a problem like it with any other vessel.
Last night when the weapon malfunction issue struck me, I tried yet again to clear it by weapon swapping (call me a stubborn optimist lol), but instead this actually had the OPPOSITE effect, and disabled a second slot, meaning for the next combat I had 2 inactive front beam weapons and only an active quantum torp launcher...
It's such an irritating bug because it's unpredictable. Is it triggered by enemy weapon fire disabling a weapon and the "Mission Pod Factor" somehow meaning the weapons remains disabled rather than coming back online? Or could it be the act of using Beam Overload with Dual Beam Banks on the Mission Pod?
We may never know...
Tis a pity because otherwise, the Recon sci vessel is my favourite to date without question.