If you check several boxes in a checkbox group, the values are stored as text in the field, separated by returns. I'm suprised that exported with the values in a single line like that.
If you want to display the same values with commas, you can define a calculation field that makes this subsitution and then you export the calculation field to your excel file:
Substitute ( YourcheckBoxField ; ¶ ; ", " )
In turns out that if I wrapped the text in Excel the data shows up in a cell with a line for each item. If anyone else has a more elegant solution I'd love to hear it.
Phil's suggestion - creating and exporting a Substitute() calculation - is the way to go. :^)