For what's it worth, here's an indirect confirmation for this bug for
Hardy.

I'm using SysCP and had problems with APS files (which would be reported
as "this is not an APS file").

http://wiki.syscp.org/docs/aps-handbook says under "PHP configuration issues" 
has this to say:
"Users of a 64bit system with PHP 5.2 must enable the PHP exec function in 
their configuration for the SysCP vHost. That's because in the 64bit version of 
PHP 5.2 exists a bug, which makes it impossible to open Zip files including 
more than 509 files. For that reason a fallback has been implemented which 
relies on the exec function of PHP. The files will be extracted in the 
temporary directory using unzip. So exec mustn't be in disabled_functions if 
you use a 64bit system!"

Applying the described fixes indeed made all the "this is not an APS file" 
messages go away.
This is fully consistent with the existence of the bug in Hardy. (Seeing the 
zip_open bug was first reported for PHP 5.1.something, this is less than 
surprising IMHO.)

I'd like to see this make its way within the next week because a long-scheduled 
hardware upgrade to a 64-bit machine will be effective then, and we may be 
unable to apply security fixes for PHP software if they are distributed as zip 
archives with more than 509 files in the root directory, and no workaround.
Not a large chance of happening, particularly since we're going to upgrade to 
Karmic ASAP, but if it does happen, we're screwed...

-- 
Compiled zip support in PHP 5.2.4 64bit can't open archives with large number 
of files.
https://bugs.launchpad.net/bugs/406303
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