Urgent help needed!!

I’m in need of some really big help/advice!!

Last night I was trying to add a link to my footer,

/includes/templates/template_default/common/tpl_footer.php

Since then I noticed that I’m receiving PayPal receipts but no order has been created for the payment -

no email was sent to confirm the order,
the order is not showing in admin,
when I click on the individuals profile it shows that they have not placed any orders.

However, the money is there!

I did a test sale and I and paid for an item, I was then redirected back to an older order that was made,

I then done a test sale for a free item and this was ok,

I have jam JROX installed and think I have done something to this but I have been looking and can’t see what I have done,

I have put the site down for maintenance while I try and get to the bottom of this problem but I’m not getting anywhere fast,

Please help!!