I had the same issue, but fixed it by deleting DUPLICATE Helvetica or Helvetica Neue fonts.
I am using OS 10.9 Mavericks, and I noticed FontBook had an error which allowed me to automatically resolve one of the fonts, particularly Helvetica. In addition, my third party font manager program, called Linotype FontExplorer X, showed the Helvetica Neue font was installed twice: once as a a system font and the second as a font to be accessed by various non-system applications. When I deselected the duplicate font—so that it was only installed once as a system font—my boxed characters disappeared and the correct font was loaded.
Once these font changes were made with my two font manager programs, I quit Chrome and then opened it again. The problem has been solved for me thus far.