Start with those warning ents - i assume "ent not found'

Check the code paths and the analyze what is the different about location and code for those ents.

If other ents are loaded and just these have and issue, then you have a logic to compare working ent loads to failing ent loads.

My assumption being that there must be a clear and obvious difference

Also because of your answer to Savin we are now sure it is not a bad ent or file, but in fact a bad location ref. I think i had this type of problem when I placed a wed ent then move the file to a new folder.