As ikegami notes, I get no problem data from your program. I tried 5.8.8 and 5.10.0 on Linux, Strawberry 5.10 on Windows, and ActiveState 5.8.8 and 5.10.0 on Windows. In every case, the generated file is identical to the source file. I also tried it with a PNG without the encoding changes on the file handles with the same results:

use MIME::Base64 qw( encode_base64 decode_base64 );
open( INBIN, '<', 'file.png' ) or die "$!";
open( OUTB64, '>', 'file.b64' ) or die "$!";
binmode( INBIN );
while ( read( INBIN, $buf, 60 * 57 ) ) {
    print OUTB64 encode_base64( $buf );
}
close ( INBIN );
close ( OUTB64 );
open( OUTBIN, '>', 'out.png' ) or die "$!";
open( INB64, '<', 'file.b64' ) or die "$!";
binmode( OUTBIN );
while ( <INB64> ) {
    print OUTBIN decode_base64( $_ );
}
close ( OUTBIN );
close ( INB64 );
[download]

I am curious what exactly is different about your ActiveState 5.10.0 and these other installations. What's your MIME::Base64 version? What's your Windows version? Are you using anything else in the mix like Windows-to-Unix compatibility tools or anything?