In the end, this was an encoding problem. When I originally split my SQL data into two separate files, the new file had a default encoding of ANSI where the original (and my database were UTF-8).
Upon changing the encoding to UTF-8, I saw loads of strange little characters which my text editor couldn't search & replace.
I set the encoding back to ANSI, created a new text document with UTF-8 and simply copy-pasted the information from the ANSI document to the new UTF-8 file.
All of the above was done in Notepad++.
Problem solved - 7 hours of diagnosing the problem; less than 5 seconds to fix.