The reasons why no color flags show for a weight group in the Method window is that no methods is defined (grey flag). Most weight groups in the standard weight breakdown structures (WBS) in ShipWeight has one or more estimation methods and the color flags are supposed to indicate whether estimation and/or plot parameter(s) (red flag) or comparison paramters (yellow flags) are missing for the current project. A green flag indicates all releveant parameters according to the estimation method is defined. 

Explanation on how estimation parameters are defined can be found in webhelp here and in the tutorial here. A chapter on how to create method sets is found in webhelp here