DGrey,

I'm assuming that you have some custom conditional actions setup for the "Over $60, over $100 etc." flat rates?

#1) What are your flat rate methods?
#2) What are the conditions / condition groups for each rate method?
#3) Which "Shipping Method" do you have enabled for the product content type? I am guessing at this point you should ONLY have "any flat rate method" enabled for what you are trying to do.