I set up camp for a few minutes next to the new bike box at St. George and Harbord in order to get a sense of how people are using them. My conclusion: the bike boxes are not different enough from before to make them stand out to drivers and cyclists as bike-only places at red lights.
Watching through a few light cycles it looked like about 50% of the drivers would stay behind the bike box. One of the main reasons for stopping in the bike box was drivers inching forward to make a left turn but hitting a red light. On a busy intersection like Harbord and St. George this happens a lot.
[img_assist|nid=4132|title=Van parks in bike box|desc=|link=node|align=center|width=500|height=375]
About 1 in 2 cars stopped in the bike box; particularly on St. George.
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The confusion is evident in this photo. Not only are the cyclists assuming they have to stay behind the bike box but the cars are actually creeping into the box. Photo by Tino (click on photo to see more). I didn't actually see any cyclists do this, so I'm assuming this is rare. Many cyclists don't like to stick behind the white line (and neither do car drivers).