If you are writing a binary file on a Windows system, you should add a 'b' flag.

 
$fp = fopen( "binary_file", "wb" );

and read them like this:

$fp = fopen( "binary_file", "rb" );

1.	Acceptable fopen() Modes
2.	Calling fopen() with a Context Resource
3.	Opening a file
4.	Opening a file on Windows
5.	Opening a remote file
6.	Opening files in the include_path
7.	Using fopen( )
8.	Using the fopen() Function
9.	File open with exception checking
10.	Getting and Printing a Web Page with fopen()
11.	Getting and Putting Files with FTP
12.	Reading a File with fread()
13.	Reading from standard input
14.	Load remote file
15.	Open a connection with the PHP site (http://www.php.net):
16.	Opening Files
17.	fopen() function opens a file, returns an integer, as a file handle.
18.	fopen() requires the file path and the mode in which the file is to be opened.
19.	fopen() returns false if the file cannot be opened for any reason.
20.	PHP 5 Arguments for Opening a File
21.	Safely reading a binary file

If you are writing a binary file on a Windows system, you should add a 'b' flag. : fopen « File Directory « PHP