I don't believe that WordPress would be stripping anything from your template file. The most likely reason is that you are not using the correct template file for the area that you are trying to edit. The templating sytem is relatively easy, but can still take a while to get used to, and the file names don't help with making things easy to tranverse, so it might take a bit of searching to find the actual template file that you want to use.
If you are 100% sure that you are using the right template file, add this at the top of it and see what happens.
echo "<p>Forced Stop</p>";
Refresh the page, and see if you get the text 'Forced Stop' right at the end of your page with nothing else under it (also check in the source code just in case). If it's there, then you are using the right template file, but if it's not there you are not using the right template file.