Well I've done a little testing, and though I've not used a cpu/ram monitor (bit burned out testing this game tbh) I can confirm
something is happening to degrade performance over time. On initial load/first flight I get no CTDs and decent performance. By the third mission (including repeats of the same mission) I get several second CTDs when accessing the Esc menu in flight. By the fourth or fifth mission I'm getting the 'Low performance - disable Aero?' dialogue, fps has dropped noticeably and stutter starts to return. Swapping between different missions seems to exacerbate the problem; staying with the same mission causes less slowdown but it is definitely still present.
There is definitely something causing an over-time performance degradation, very possibly the aforementioned RAM not clearing after a mission. I'm highlighting this so Luthier & co see it, hopefully they'll be able to identify just what it is that's causing the problem and fix it!
EDIT: finally tried a proper test and ram usage goes from 63% on the first flight to 78% by the fourth or fifth.
