I tested on my Moodle 3.6.1+ (Build: 20181220) with 3 PDF's. All three were converted and I could mark on all three of them. I just upgraded the to Moodle 3.6.2+ (Build: 20190208) and using a student uploaded two PDF's and an odg file. The first student acount still showed the rendered and annotated 3 PDF's. The new student upload rendered all three files correctly, I cound annotate on them, and the student could see the results.
Do you have any restrictions set for Submission types > Accepted file types, in the activity setup?
Under Site administration > Plugins > Document converters > Manage document converters, are the file types you are trying to use, all listed under Supported document conversions column for Unoconv?
