We should probably URL Encode your Base64 string on the C# side before you send it.
And URL Decode it on the php side prior to base64 decoding it.
C# side
byte[] encbuff = System.Text.Encoding.UTF8.GetBytes("the string");
string enc = Convert.ToBase64String(encbuff);
string urlenc = Server.UrlEncode(enc);
and php side:
$data = $_REQUEST['in'];
$decdata = urldecode($data);
$raw = base64_decode($decdata);