Pictures are always helpful, but the most likely explanation is that your levers come with dished boss covers for a standard 28.6mm steel downtube, and you need the flat boss covers that work with the flat lever mounts on fat-tubed bikes.
Refer to the diagram here:
http://www.unc.edu/~cupery/pics/bike_pa ... covers.jpg
I suspect you've got the curved part 6 from the main diagram, and you need the flat part 6 from the small option box in the lower left. Does that look right?
Calmes dans le demi-jour
Que les branches hautes font,
Pénétrons bien notre amour
De ce silence profond.