After Installing SUPEE-9767 there is an issue with the new jquery 1.12 that was added. The patch replaced the 1.10 version in /rwd/default/layout/page.xml that was under "Add vendor dependencies" (lower in the stack) and added 1.12 higher up in the stack just under prototype.js.
https://www.diffchecker.com/MwGkgPsK (original 1.9 on left, Patched version on right)
When the js files are merged under Configuration > Advanced > Developer it breaks the onclick events for the order button on product pages and the header links up top (cart, account, etc). Maybe other things as well as it generates a lot of errors in the chrome console for cookies, VarienForm, element.attachEvent, Translate... etc. When the .js is not merged it works as per normal.
Modifying /rwd/default/layout/page.xml to move 1.12 back down to 1.10's old place lets you merge the .js and have it work as per normal.
