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On one computer I use, my emacs will always run commands in my home directory, rather than the directory of the currently open file (i.e. default-directory).

A standalone reproduction is executing the following:

(let ((default-directory "/tmp/")) (compile "pwd"))

On the computer in question, it prints the path to my home, not /tmp as it does on all other computers-with-emacs I have access to. (The same thing happens with M-!/M-x shell-command.)

I recently installed 24.5 into my user folder (the global install is 23.4), and installed Emacs Prelude but the behaviour described above happened/happens in all configurations (it certainly happened before I made any modifications) and happens if I run emacs -Q (for both 24.5 and 23.4) to avoid reading my configurations (as lawlist asks).

If there's no obvious problem/fix, is there a good way to start to debug a problem like this?

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    Does it happen when you start Emacs with absolutely no user configuration whatsoever? Emacs -Q If not, then consider bisecting your user configuration (commenting stuff out) until you find the culprit. – lawlist Oct 7 '15 at 0:08
  • @lawlist, yes, it does still happen unfortunately. – huon Oct 7 '15 at 2:27
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    Looks like your shell is doing something. What OS are you running? What shell? What happens if you start a new shell in a terminal in a non-default directory? Try running your shell with the -x option if it's a typical Unix shell (bash, zsh, tcsh, …). – Gilles 'SO- stop being evil' Oct 7 '15 at 14:27
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After experimenting with overriding $HOME and tracking some things through with bash -x as @Gilles suggested, I found my ~/.bash_profile included an isolated cd command, meaning the shell emacs spawned to compile/run commands was always left in my home directory.

(Annoying, and apparently my fault, although I have no idea how that cd got there.)

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