Running the 2015.3 AE and latest updates for everything as of this posting. W7x64.
I've noticed that while working with AE or not, AME runs in the background at full CPU and I/O Priority, which defeats the whole purpose of being able to run in the background and continue working. I use several effects from Red Giant, Genarts, Videohive and Zaxwerks to name a few and it makes my machines unusable unless I use task manager to manually set the priorities lower. I've tested this on several machines and all behave the same.
Hard to understand why this would be planned behavior, is there a setting I've missed somewhere? If not, it would be a useful feature.
I use several effects from Red Giant, Genarts, Videohive and Zaxwerks
You know, half of those effects are GPU accelerated and will either run on full throttle on the GPU or fall back to CPU-based rendering, either of which naturally will put considerable strain on your hardware. Not saying that AME shouldn't behave more gracefully, but it seems you are expecting something that is not possible because it's out of the control of the AME process itself. you could of course try to experiment with settings like turning off GPU usage in AME itself or setting Sapphire to forced CPU mode, but this naturally will lead to longer rendering times...
Just another issue to deal with...piled on top of the already mile high heap of never ending workarounds I have to endure with Adobe. Lol, now I'm actually requesting features to help me do it!
Oh and did I mention not all the plugins render properly after the 2015.3 update forcing me to render through the main program and this losing even more time? Sure hope some fans lecture me on how nothing is Adobe's fault and I should be happy with what I get.