When you map FrameMaker files to CHM files (see §9.15.1.2 Mapping FrameMaker files to CHM files), by default Mif2Go first checks for the presence of a FrameMaker file with the path specified in [ChmFiles]; if the file is not found, Mif2Go checks for the file without a path.
To require Mif2Go to use the path:
; RemoveChmFilePaths = Yes (default) to try to match filenames
; without their path component in [ChmFiles] after trying with it,
; or No to require the path (with forward slashes)
; to be present on the left-side names.
§9.15.1.1 Specifying the default CHM file