This is an old old bug leftover from GDE. In blnalign and blpalign, the first part of the shell command for all the Phylip programs read as follows:

tr ""~"" ""-"" < %in1% | sed ""s/[:_]CDS/_/"" | readseq -a -f12 -pipe | sed ""s/ YF//1"" > %in1%.tmp;

the "| sed ""s/ YF//1" part would delete " YF" from any sequence in the Phylip alignment file. This would occur rarely ie. YF preceeded by a space, which is why it was not discovered until now. Anyway, the code has been fixed for all Phylip programs in blnalign and blpalign.