And then, an answer presents itself! I pulled the input file out of the directory where the .m files were stored when it was compiled, and placed it elsewhere. This allowed me to remove the file from the list of "Files required for your application to run" section. Then I added the file (from its new location), to the "Files installed for your end user" section, and compiled the code.
The input file is loaded when the compiled code is installed, and I've checked that it is the file being read by the code by removing it (removing it causes the .exe to generate an error).
I have no idea why this worked.