Extreme Variability in Render Time Durations

So I have a 20-second clip I'm exporting from After Effects through AME. It's a 3D video, with 35 total assets on the video. 

Computer is new and souped up for what I'm doing, so I'm not worried about specs. All my drivers are up to date, Windows is up to date, all software is up to date, everything is running fine on my computer. After Effects runs like a dream, but Adobe Media Encoder is gradually becoming a nightmare. 

I've rendered the video a dozen times already, with edits and whatnot, each time taking roughly 1-2 minutes - which is about what I'd expect, given that a 7-minute 2D animated video took about 5-10 minutes. Though halfway through the week the render times went from 1-2 minutes to 1 hour 20 minutes to 1 hour 30 minutes. 

AME uses 99% of my CPU, jumps RAM usage up to 92%, and disk usage to 30% by itself. So it's definitely using what's there - and that's about the performance I get when it takes 1-2 minutes to render. Though running my computer for an hour at that usage seems potentially dangerous for the hardware - yesterday my screen blacked out for 5 minutes in mid-render. 

AME has worked perfectly fine on this computer for months, but this just suddenly became an issue when I got on Thursday morning.

So to keep it simple;

• Why is AME taking over an hour to render a video that took 1-2 minutes to render a few days ago?
• What can I do to fix it? Any workarounds?