This is a problem I've had for at least two years (actually can't remember how long), but it's finally irritating me enough to post about it.
As a whole, GPU acceleration works really nicely on my system. I have an Nvidia 1060 6GB card, 32GB RAM and a Ryzen 7 3700X. The video editing I do is for gaming stuff on YouTube, rarely anything more complex than some cuts and adding an audio track. I export everything using GPU-accelerated H.264 and it flies along beautifully fast; a ~20 minute video at 1080p60 will render in about 5 minutes.
Unless it features cross-dissolve. Now, unless I'm sorely mistaken, cross dissolve should be a GPU-accelerated effect, and indeed it works beautifully when editing in the timeline. But when I go to export - whether through Premiere Pro, or the Media Encoder queue, every time there's a cross-dissolve, performance absolutely tanks. If I monitor hardware usage, GPU drops to 0%, CPU rises to 100%, and it takes about 15 seconds to render each 60-frame transition. That's 4 frames per second, which cannot possibly be right.
The footage itself is recorded as an .MKV file, which Premiere Pro won't touch, so I pre-process it first in Handbrake to a .mp4 using the NVEnc implementation of H.264.
From Googling over the years, I seem to be the only person that's ever had this issue. I really hope I'm just being thick and there's an option I'm missing, but it's so bizarre that cross dissolve works fine in the timeline, but not in Media Encoder, and that GPU acceleration works find in Media Encoder except for Cross Dissolve. I've not got "render at maximum depth" selected, and all my GPU drivers are up to date.
If there's any advice for how to go about diagnosing or solving the problem, that would be super helpful. I've attached a 30-second sample of footage, a project that uses it in two timelines - one with cross dissolves, and one without, and the render log. As this shows, the one without cross dissolves renders in 7 seconds, the one with takes just over 1 minute.