You have of course checked the simple things; are all your binaries executable (you know chmod +x ...)?
Second things: you say they work in a fixit shell: is this with the fixit CD in place? If so, perhaps your binaries uses dynamic libraries? I'm guessing that wouldn't do well in the mfsroot image; all programs mus be statically linked there. Or am I wrong about that?
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Torfinn
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