So it seems that with 3.5.1 combined with my theme (SimpleDark) and Jetpack, all AJAX features are broken now. For example, typing the search box doesn't fade the word "Search...". Also, you can see boxes around my star ratings which is not intended. The top menu should shift to the right, above the second column. Disabling Jetpack resolves the issue. This started happening last week which is when I am pretty sure 3.5.1 was released so I am not 100% sure if it is WordPress, Jetpack or my theme. It has been working fine for the month I have been running the blog.
Any insights are very much appreciated.