I am broken! Well, maybe not me specifically, but I don't see this issue when looking at other people's reputation pages/graphs, so this isn't something specific to the browser I am using.
This issue only seems to occur in Google Chrome 31 and 32 only (the main browser I use). I tested it in Firefox 26 and Internet Explorer 10 and 11 and could not reproduce it.
So here is my reputation graph, as seen here:
As you can see, the reputation history graph along the bottom is white, but if you look at the selected bit you can see the white outline of the bars.
Here is a closer look:
So the bars are definitely there. If you select enough of a time frame using the graph at the bottom, the problem also affects the graph at the top as well:
This shows up as complete white just like the bottom graph until you start to mouse over the bars (which causes the little pop up detailing how much reputation you earned on that day).