File problem when uploading to server

Hi does anyone had the problem when uploading a file the code on that file just uses one line for the whole code ?.
It seems to do it on every server am with and its causing me a headache.

sample of file after upload
<div><?php code go here ?></div>

But should be like this...
<div>
<?php code go here ?>
</div>

I use ftp filezilla also tryed cute ftp