Something like this: 

<a class="<?php if($page=='test') echo 'active'; ?>"> href="?page=test">Link</a>

causes an "Error in the code" message on saving. I think, your built-in code-checker should tolerate php, or at least it should be possible to deactivate this error message.

By the way: Code-higlighting for php would be great. Even just making the text from <? to ?> generally appear in another color, would make Amaya much more useful for me and my course participants.