This issue occurs in the latest version of Media Encoder and the one before that.
Screenshots attached. When I render in Premiere, my RTX 4080 S is at ~80% usage, intel iGPU at ~20%, and i9 14900k at ~30%.
When I render the EXACT SAME sequence in Media Encoder, the RTX is at less than 10%, no iGPU usage, and slightly less CPU usage.
Exporting to a MP4 UHD 30mgbp file, Windows 11, footage is on a Samsung T7.
P.S. The Renderer is set to CUDA and I set the encoder/decoder settings in the preferences to ON. This issue with render speeds came up recently without me changing any of the settings.
Also, there's barely any effects on the timeline. It's just a few Lumetri Color effects and a logo with a blur.