Hmm... Not sure what is happening. In iTunes, you should be able to figure out what type of compression is used for any entry using "Get Info." Select a track, right click, select "Get Info," and see, on the summary page, what it says right under where the album art would be following "Kind." It should say "Apple Lossless audio file" if the directory entry is, in fact, Apple Lossless. If its an AAC file, it will say "AAC audio file" instead.
Since iTunes labels both AAC and ALAC files with the ".m4a" extension, I am guessing that the .ALAC file is being created somehow by EAC. Are you using iTunesEncode? My iTunesEncode settings are found under EAC > Compression Options... > External Compression. I have "use external compression program" checked, parameter passing set to "user defined scheme," use file extension set to ".m4a," program for compression set to "C:\Program Files\EAC\iTunesEncode.exe," and additional command line options set to "-e "Lossless Encoder" -a "%a" -l "%g" -t "%t" -g "%m" -y %y -n %n -i %s -o %d."
What are your settings showing?
Since iTunes labels both AAC and ALAC files with the ".m4a" extension, I am guessing that the .ALAC file is being created somehow by EAC. Are you using iTunesEncode? My iTunesEncode settings are found under EAC > Compression Options... > External Compression. I have "use external compression program" checked, parameter passing set to "user defined scheme," use file extension set to ".m4a," program for compression set to "C:\Program Files\EAC\iTunesEncode.exe," and additional command line options set to "-e "Lossless Encoder" -a "%a" -l "%g" -t "%t" -g "%m" -y %y -n %n -i %s -o %d."
What are your settings showing?