I can't give you a complete answer, but I believe the "rt" mode is supposed to open files in "text" mode. On cygwin, and maybe mingw, this makes an attempt at giving consistent results for mixing unix-style LF line endings, and DOS-style CR/LF endings (and maybe Mac-style CR endings?). It's one of the little things that often cause trouble in porting between *nix and windows - using "rt" is an attempt at easing these problems, although it might cause some of its own.
Aha! That would explain why switching to binary mode (we are opening an ELF or BIN file) solved the issue, at least on windows.
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