This sounds like the browser is caching it and using the cache first, right? I suggest you have the link generated by php code with a random ID. Say the link is to main.php- have the <a> tag be:
<a href="main.php?<?PHP echo rand(0,1000); ?>">Home</a>
... so the main.php script would be passed an pseudo-random number every time, causing it to reload from the server every time (in most browsers).