As mentioned, I was running a solo Archon hunt spy mission and had some epic stutter - every 10 sec game would freeze for about 0.5 sec.
That being said, as soon as I solved the last lock (remember, those are the Narmer-specific ones), the stuttering instantly stopped and did not appear even once until the end of the mission.
IDK if those two are connected in any way (seems obvious they are), but hopefully it could help tracking down the issue.