Phenotypes subsetted twice in scantwoF

In scantwoF it appears that phenotype columns were being subsetted twice when n.perm>0.  Jane was getting an error when trying permutations. Made a small change to remove one of those subsetting operations.  We have not tested this well, but we don't get the error message any more.  Comparing with scanoneF reveals that the code for the two functions are slightly different in the way they deal with phenotype subsets.

Also, I am not sure if I am doing this pull request right.  Pardon my clumsiness... Github seems to be flagging more changes than I have made.