So I’ve done some testing, and updated to word press version 4.6.1. With the update the company logo setting is working, it’s removed the logos.
However I have noticed that the problem with the application fields occurs whenever I hit the update button after first publish. I don’t even need to make any changes, if I publish a job listing it all shows up fine, but once i hit update it stops showing half the fields and changes their settings to text fields.
I’ve done as you suggested and created these fields in the main settings, which has worked.
However, when I try to add any detail through the individual job itself, say adding a feature such as salary, it seems to break the job listing and once again only show 2 out of the 5 fields and changes their settings. This also happened when i tried adding a company logo or any other details to the job. I haven’t modified anything in the plugin, I did select the option to show job listing without company logo, however it seems it is still showing the company logo even when no image has been uploaded.