I've been recently having a problem with Adobe Media Encoder CC 2017 after the update from 2016 to 2017.
I would honestly appreciate it if someone could help me solve this issue.
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Are you queuing the export from Premiere Pro to Media Encoder? Is this happening only with Premiere Pro exports?
If yes, In Media Encoder > Preferences > General > Premiere Pro > Uncheck "Import sequences natively" & queue the export.
Please let us know the status.
Sorry, but it didn't work and yes, it is from Premire Pro to Media Encoder
Are there any .mp4 files in the project?
In Media Encoder > Preferences > Media > Uncheck "Enable accelerated Intel h.264 decoding"
Restart Premiere Pro & Media Encoder, Queue the export again & test.
If issue persists,
Create a new project in Premiere Pro, Import the old project file(.prproj) into it & queue the export.