Because they are too big. A double stack bolt holds together 3 pieces of metal: the big ring -- the crankarm spider -- the small ring.
When you run one chain ring, you eliminate one of the pieces of bread in that sandwich. And your bolt is too long. Which you've found out yourself.
I suppose you could McGuyver yourself a fix with some washers or something. Or you could get a set of single stack bolts (just $6 or 7 at your LBS or online) you get the parts that fit just right and save yourself a huge headache. That was my experience anyway.