I'd like to know too. I know I've asked in the past without getting any answers.
I almost think it's something to do with code pages that are installed. Remember that a box is what Windows uses if it doesn't know what a character is. This is not only true for fonts, but also for code pages. For example, if Ctrl-B "character" was that little "L" shaped thing in one of the Asian code pages I have installed, then that may be why I don't have it as squares anymore. Perhaps that is the same for you as well?