I managed to solve this. The problem stems from the XML file that PluralEyes creates. The file appears to be missing information telling Premiere what codec settings to use for the sequence.
Open up your PluralEyes export in a text editor (I use Notepad ++). Do a search for the word “sequence”. You’ll see something similar to the following line, just above a yourproject.MOV_synced tag.

Highlight the entire line and replace the text with the following code. (Code link at bottom of post)

You’ll need to do this twice, one for the opening sequence and one just above the yourproject.MOV_synced Replaced tag as below.

Save the file then go back to Premiere and import as normal. It should be working fine now.
NB: I’ve uploaded a text file here with the code to save you typing it out. 8297_pluraleyeserrorfix.txt.zip
Good luck.