The first step in a classification is to create a raster or a Grid stack of the bands that are related to be used in the classification. Also needed is a signature file, which defines the statistics of each class that will be used in the classification. The signature is created from training samples in a supervised classification and specified statistical groupings in an unsupervised classification. The input raster or Grid stack and the signature file are input into the classification to perform either a maximum likelihood or a class probability classification. If the same bands that were used to create the statistics for the signature file are different than the bands used in the classification, inconsistent results will occur.
Make sure that the bands used in creating the signature file are the same as the ones used in the classification. More information on producing signature files is available in the help.