After some noob discussion over at "gbafail", and after I made my own observations, I came to the conclusion that the parsing of bootmii.ini might a little bit buggy - but before I explain the possible bug, I must add that BootMii is a very fine piece of homebrew software, and the bug I might have found is merely an annoyance, nothing really severe.
From testing, I have deduced that Windows-style line endings (0x0D0A) in bootmii.ini caused the file to be ignored. Furthermore, even after changing the file to have Unix-style line endings (only 0x0A) instead, it was still ignored if the last character was not 0x0A (but e.g. "U" from "SYSMENU"), which is common only in some environments, but not in all...
I highly appreciate your work and hope to have been of help.