I’m sorry, I know the title isn’t as specific as anyone would really care for, but this is a very odd problem and I don’t know how to concisely encapsulate it for a title.
I typically use the US English/Macintosh layout because there’s assorted characters and sometimes (though not always) accented letters I like to be able to type. Anyhow, what I’ve noticed is there are some places that I cannot get it to work but only partially. So, for example, if I’m naming a file, or if I’m in the Gnome text editor, or in the terminal (Console) and probably other places as well, some AltGr-summoned characters will work (for example, I can type the ß character) but a lot of others won’t type. However, if I’m in other programs such as Firefox, or xed, or Scribus, or GIMP, or etc. etc., all the characters that wouldn’t type, do.
Now, I think that there may be a misassignment here of the keyboard layout, but I cannot for the life of me really narrow down the root cause, because everywhere I know to look, I can’t find anything amiss.