Adobe changed the folder structure for the presets files, again, which is a huge pain in the ass when migrating to a newer version of Premiere Pro, etc. Especially when the presets are not carried on automatically (as they should!)
Navigate to your current presets folder and copy all the presets you’ve got there into your clipboard.
Then navigate to this folder:C:\Users\<username>\Documents\Adobe\Adobe Media Encoder\11.0\Presets and paste them there.
Done, now your presets will show up in Premiere Pro CC 2017 as well as in Media Encoder CC 2017.