I was seeing the very same symptoms as Andy but was able to solve the problem.
In my case, the issue was caused by the fact that I had multibyte string function overloading enabled in php.ini (configuration directive mbstring.func_overload). As a result, ezcArchive became confused so that it could only see some of the files in the site package (and in any tarball, for that matter).
The "Site package selection" step during installation was failing because eZPackage was unable to find package.xml even though the file was there.
The bottom line: mbstring function overloading and ezcArchive do not seem to play well together.
I cannot install 4.5 beta1 due to this issue, and checking various symptoms posted here since 2006 (!), including those above, have yielded fruitless too. So, bump.
Edit: Oops, mbstring.func_overload = 0 was not in my dev php.ini. Fixed!
A good candidate for a feature request then: add checking for mbstring.func_overload in the setup wizard. Anybody wants to write this down in the issue tracker?
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