Elite: Dangerous PvE - Mobius

Just what it says on the tin, I've tried everything from graphics drivers reinstall, re seating my ram, GPU, and even did a dust up and clean up of the case and old software. No dice. I see no change in gpu usage or cpu usage when it occurs, and it happens so fast it doesn't even register on FPS counters. The issue happens at all times in game, even at the main menu you can see the rotating station in the back ground stutter.
This wasn't an issue for me until about 2 updates ago, and has stuck with me ever since. Changing graphics settings makes no difference at all, even at minimum. Really at wits end here, It has made fighting without gimbaled weapons impossible, and I frequently over shoot things or slam in to the station floor when docking due to the stutters.

What CPU, GPU etc do you have Pembroke?

pardon for not posting that already, it's an "older" machine but still capable of play, the cpu is an AMD FX-4350 quad core, @ ~ 4.2 ghz, the gpu is a first revision GTX 570 Direct CU from Asus, with that lovely cooler that consumes 3 slots on the dang board. I don't seem to have any issues in other games, and I'm currently pointing a laser thermometer at the thing just to find out if there's hot points around. Not much luck, this thing's heat is pretty uniform.
I would also like to add, I get between 120 and 170 fps

This sounds more like something system related than a problem with your rendering. The fact that you aren't seeing an FPS hit (metric wise) supports this, as well as it suddenly cropping up. I would investigate your background processes... try shutting off anything unnecessary to run Elite including anti-virus scanners or similar. If you're running Windows 7 or 8, open the resource monitor and see if you notice anything. I'd pay close attention to your disks, see if one of your internal disks are showing spikes in activity or if one is being overloaded. I/O related issues are a lot harder to track down than other issues, even if you have an expensive motherboard they tend to choke even if only one disk out of several is under heavy load.

Another thing to check is your power management settings. Make sure you choose the power plan with the best performance, try disabling any profiles that throttle graphics, disk or CPU.

All of that said, try a fresh restart. I've had issues like you describe before, but generally on a laptop where power management and I/O are a lot more strict and sensitive. The cause usually was disk in those cases.

EDIT: I am a certified technician for computer repair, though I don't do that for a job anymore. Just an FYI, sometimes I can get too technical so if something doesn't make sense let me know.

Oh I totally understand, I've been running threw monitoring as well, I noticed spikes in disk activity, so last night I reinstalled the game on my SSD (if that doesn't fix I/O lag, I don't know what will) this has also carried over multiple restarts. My power management settings are always on high performance on my desktop. I had similar issues to this back in Skyrim when it was installed on a RAID, installing it on a single disk fixed the issue for some reason, but it hasn't seemed to effect the issue in Elite.
I went threw background processes after I read this and killed some things, I simply use Microsoft Security Essentials for an antivirus on this machine. I Just can't seem to find any sort of culprit. It is very baffling, especially since the lag increments are perfectly regular.
(electrical engineering major here, computers aren't exactly my core focus but I know a bit here and there, still wouldn't consider myself any sort of expert though)

Just a blind question - does it same in tutorial missions? Just for a case it is network related issue (game waiting for packets blocked by router, etc.)...

yeah, even in single player training.
starting to wonder if a failing ram module might be causing it... I'll start pulling pairs and trying the game to see if that causes a change in the next hour

Update on that, I've seen no difference with ram swapped around... I don't think that is the issue

Hmmm, my next guess was CPU or GPU overheating, but as you mentioned above temperatures seems alright... so no other idea. Unless it's temperature was uniform, but very high.

Edit: I just spotted elsewhere that some game has issues with controller (gamepad), causing stutters in short intervals. So it may also worth a try, removing all peripherals...

only peripherals attached is my keyboard and mouse, keyboard is PS/2 plugged, so interrupt based, and the mouse is just a plain USB mouse, I can try swapping for another
I'll give it a shot shortly
edit: Yeah, no difference there sadly.