SD,
It sounds as if the bolt heads were too thick for those dust caps and the Campy crank. I have had this problem once and did the same thing (sanded the heads of the bolts to make them thinner) because the bolts were from the hardware store and not specifically for cranksets. If this is all you needed to do, you are good to go and don't need to replace the BB.
If you feel as if you need a pair of bolts which are specific for cranksets, you can get a set here:
http://www.loosescrews.com/index.cgi...d=886600711944
Best of luck.