Is it possible the match field in file B is unstored?
A quick question: you use the word "file" above. Do you mean table? I'll assume that you mean table.
I raised my eyebrows at this line: "Files A and B have multiple occurrences of the match fields but that has not been a problem in the past."
There isn't enough information to give a diagnoses, but it is possible that there should be a join table in there? Take a look at the FMP documentation on join tables, and you might look at YouTube for a video demo of that. There are several short demos. It might just solve this.
Thank you for asking about the storage option for the offending field. First of all, the match fields in all of the files (A, B, and C) are calculations, a concatenation of a town and a school name. In checking the storage options (indexing) for the offending field, I discovered that I had long ago defined that field as a number (FileMaker's default for a calculated field). Once I changed it to 'text' everything now works fine. Prior to using that field as a match field between two separate files, the field definition (number instead of text) did not have an adverse effect. Thank you.