PluralEyes creates some configuration files that Adobe Media Encoder uses, and they can get corrupted.

To solve the problem,

• In Windows Explorer, navigate to
  
  %appdata%AdobeAdobe Media Encoder5.0, or
  %appdata%AdobeAdobe Media Encoder4.0
  depending on which version of Premiere Pro you have.

• Delete these files:
  
  AMEPrefs.xml
  batch.xml
  Watch Folder Info.xml