well, one thing for sure is that EM doesn't see, or look inside, folders. also, if the file type isn't on the "this is a startup document" list that EM has, it won't show up either. examples of things on the list are: INIT (most normal extensions), CDEV (most normal control panels), PRER (chooser printers), shlb (shared libraries), RDEV (chooser networks i.e appletalk or dave)
the majority of those that are conspicuously absent are "thng". I have no idea what, if anything, that's short/stands for.