Well that explains some things. One copy--the one that used to be .alac--was being created by EAC and I suspect the other--the .m4a--was being created by iTunes. Is "copy file to iTunes directory checked" in iTunes > Preferences > Advanced?
EAC has its own directory to write too... Check EAC > EAC Options there is a "Directories" tab--the directory shown is where EAC puts things. Not sure what would happen if you made it the same directory as iT...
EAC has its own directory to write too... Check EAC > EAC Options there is a "Directories" tab--the directory shown is where EAC puts things. Not sure what would happen if you made it the same directory as iT...