Farms2, I even found other "prototype.js" from other themes. It is identical, replaced it even, solved nothing. But. . .
Borrow K2s prototype.js.php and put into Tarski's js folder.
I'm guessing it is not so much a flaw in prototype.js, but how or when it is called by Tarski.
I put the following into Tarski's header.php just before the wp_head():
<script type="text/javascript" src="<?php bloginfo('template_directory'); ?>/js/prototype.js.php"></script>
Oh, and deleted the prototype.php line from Tarski's functions.php.
All saves work. All headers work.
Tada.(Until I hear what else I've broken)