Please try using this CVS snapshot:

  http://snaps.php.net/php5.1-latest.tar.gz
 
For Windows:
 
  http://snaps.php.net/win32/php5.1-win32-latest.zip

No feedback was provided for this bug for over a week, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".

Same problem here using PHP Version 5.2.5 (x64) with Windows XP 64bit Professional Edition.

Duplicated files every 65535 files read using scandir(). I think you should put an alert on manual page:
http://php.net/manual/en/function.scandir.php

Please try using this snapshot:

  http://snaps.php.net/php5.3-latest.tar.gz
 
For Windows:

  http://windows.php.net/snapshots/

No feedback was provided for this bug for over a week, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".

Same problem reproduced
PHP Version 5.4.4 Windows 7 x64
PHP Version 5.3.13 Windows 7 x32

But all PHP methods listing files are affected scandir, glob, DirectoryIterator.

Reproduce code:
---------------
// Settings
$dir = './test/';
$totalFiles = 1e5;

// Create empty files
!is_dir($dir) && mkdir($dir);
for ($i = 0; $i < $totalFiles; ++$i) {
    $filename = $dir . str_pad($i, 6, '0', STR_PAD_LEFT);
    touch($filename);
}

// Glob
$files = glob($dir . '*');
echo 'glob: ' . count($files) . '/' . $totalFiles . PHP_EOL;

// Scandir
$files = scandir($dir);
echo 'scandir: ' . (count($files) - 2) . '/' . $totalFiles . PHP_EOL; // . and 
..

// DirectoryIterator
$it = new DirectoryIterator($dir);
echo 'DirectoryIterator: ' . (iterator_count($it) - 2) . '/' . $totalFiles . 
PHP_EOL; // . and ..
unset($it);

Expected result:
----------------
glob: 100000/100000
scandir: 100000/100000
DirectoryIterator: 100000/100000

Actual result:
--------------
glob: 100001/100000
scandir: 100001/100000
DirectoryIterator: 100001/100000

The problem is in readdir_r()[1]. If dp->offset != 0
FindNextFile() is called, then dp->offset is increased. Finally,
the directory entry is composed and "returned". However,
dp->offset is a short int[2], so once for every 65535 entries
FindNextFile() is not called, but a directory entry is added
nonetheless. Furthermore, dp->dent.d_off is not correct for high
values.

[1] <https://github.com/php/php-src/blob/php-5.6.9/win32/readdir.c#L92-L118>
[2] <https://github.com/php/php-src/blob/php-5.6.9/win32/readdir.h#L35>

Can reproduce bug with PHP 5.5.12 (cli) (built: Apr 30 2014 11:20:58) in Windows 7 Home Premium x64, build 7601.

I thought I was going crazy. My 100,000 files generated an array with 100,001 indexes. Took forever to find out why my script was trying to copy more files than there were in the directory.

I've made a respective PR.

Re-opening, since this issue has been re-introduced by commit
758af77[1] affecting PHP 7.2 and up.

[1] <http://git.php.net/?p=php-src.git;a=commit;h=758af77e9d1c3c6e5aea365bc0d35c385278ad5a>

Any progress on this and can this be added to tests when run on Windows?

Unfortunately, this cannot be fixed in a PHP revision, because it
requires to change the definition of struct DIR_W32[1], what would
constitute an ABI break.

I'll check whether a test would be viable (it'll likely be very
slow).

[1] <https://github.com/php/php-src/blob/php-7.4.5/win32/readdir.h#L27-L34>