In Boston, a fight over municipal pensions seems to be at odds with a nation that has taken aim at public employee benefits. The debate at City Hall is not over cuts, but rather how much retiree’s checks should grow. Mayor Thomas M. Menino wants to augment the annual cost-of-living increase by $30 to $390 a year. City Council President Stephen J. Murphy has pushed for more. Other cities and towns in Massachusetts have had similar, seemingly counterintuitive debates.