Presuming some form of *NIX if you're completely at a dead end sometimes using strace (or dtruss on OS X) can be enlightening. For something like this you're mainly interested in the lists of files which it tries to call open(2) or stat(2) or the like on. Run on both machines and then compare the two; sometimes it helps to do some post-processing to remove differences (common things would be to smash out the exact file descriptors run returned or addresses of buffers passed and get (say) a list of the files it can or can't open; possibly run those lists through sort and uniq before diff'ing can help).
Edit: a word.
The cake is a lie.
The cake is a lie.
The cake is a lie.
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