I unzipped the .mmap file and in the XML I found links of this form:
Url=""..\..\parent-folder1\parent-folder2\file-name.mmap"" on the "not working " links
Url="..\parent-folder2\file-name.mmap" on the good links.
The extra characters in the not working links are not visible in MindManager when I Ctrl-K.
However I have just spotted that the not working links have either:
Options - Source File: Copy file - create relative link OR Do not copy file - create relative link
and the good links have Do not copy file - use link as is
I think this is a DeJaVu moment and may be a result of using an old map as the basis for a new one which had the same issues. Aagh!