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.
Hi, the diff has expired but moving the file to the previous location seems like a good solution here.