I found in my 2.6 install was missing the linapple.conf file in /opt/retropie/emulators/linapple there was a symbolic link to linapple.conf in /opt/retropie/configs/apple2 but the apple2 directory was not there so it had no config file on starting up the linapple emulator. I created the missing directory and copied the sample file into the apple2 directory and linapple would then start.
Hope this works for you guys…