I only took a glance at the log but it looks like your N64 launcher file is actually the settings file instead:
[2018-01-24 22:48:05] [INFO] [Configuration] Importing "/home/acer/Desktop/RetroFE/launchers.linux/Nintendo 64.conf"
[2018-01-24 22:48:05] [INFO] [Configuration] Dump: "launchers.Nintendo 64.list.includeMissingItems" = "true"
[2018-01-24 22:48:05] [INFO] [Configuration] Dump: "launchers.Nintendo 64.list.extensions" = "zip"
[2018-01-24 22:48:05] [INFO] [Configuration] Dump: "launchers.Nintendo 64.list.menuSort" = "yes"
[2018-01-24 22:48:05] [INFO] [Configuration] Dump: "launchers.Nintendo 64.launcher" = "Nintendo 64"
The log shows you actually selected the Amstrad GX4000 from the main menu, not N64.