I can't reproduce that... so I can't fix it. Maybe you can if you dig your box following directions.
Alt-F services are started in two steps:
1-Alt-F has some services built in the firmware, such as samba, ftp, nfs, etc, and they start if enabled as soon as the box boots, even with no disks attached.
2-When disks are recognized or plugged in and its filesystems are checked and mounted, when the first Alt-F folder is found on one of them the second "boot" step starts, and the enabled on-disk services are started.
If a service is already running, because it also exists in the firmware, it is restarted, so the previous version on the firmware stops and the new installed on disk can be started.
After this second step it is difficult to distinguish what comes from disk or from the firmware, as the folders and files existing under /Alt-F shadow the ones already existing. You shouldn't touch anything under /Alt-F without special precautions.
So, /Alt-F/etc/init.d/ only contains initscripts from disk-installed packages, and those are the ones that will be started if enabled:
[root@DNS-323]# ls -l /Alt-F/etc/init.d/
-rwxr-xr-x 1 root root 1968 Sep 22 17:36 S13modload
-rw-r--r-- 1 root root 1171 Mar 18 2015 S20dbus
-rw-r--r-- 1 root root 577 Nov 21 2016 S20hddtemp
-rw-r--r-- 1 root root 1432 Mar 18 2015 S50avahi_daemon
-rwxr-xr-x 1 root root 1489 Oct 23 14:31 S51netatalk
-rw-r--r-- 1 root root 1237 Oct 18 19:31 S62dropbear
-rwxr-xr-x 1 root root 1556 Oct 18 19:31 S62opensshd
-rw-r--r-- 1 root root 516 Oct 20 03:03 S81entware
But they appear also under /etc/init.d because of the shadowing process (better, folder unioning, handled by aufs.sh). That is the source of many confusion(*)
/var/log/hot_sh.log shows you what happens when a filesystem with an Alt-F folder is discovered:
[root@DNS-323]# cat /var/log/hot_aux.log
DATE=Mon Oct 23 14:40:11 WEST 2017
PATH=/sbin:/usr/sbin:/bin:/usr/bin
hot_aux: Start fscking sda2
hot_aux: Finish fscking sda2: fsck 1.41.14 (22-Dec-2010)
/dev/sda2: clean, 17958/19505152 files, 1397462/78011088 blocks
hot_aux: Users directory found in sda2
hot_aux: Public directory found in sda2
hot_aux: Alt-F directory found in sda2
hot_aux: Stopping modload: OK.
hot_aux: Restarting netatalk:
Starting dbus-uuidgen: OK.
Starting dbus-daemon: OK.
Starting avahi-daemon: OK.
hot_aux: Restarting sshd:
And a /var/log/netatalk.log appears (not in your case).
Notice that avahi is a requirement for netatalk (and dbus a requirement for avahi), doesn't matter if they are enabled or not. When netatalk is stopped both will be stopped in the correct sequence and when netatalk is started they will be started in the correct sequence.
If dbus can't be started by whatever reason, then avahi will not be started, and netatalk can't be started.
You can see the current state of any service just typing rc<service> [status|start|stop|restart|enable|disable|...], e.g. 'rcdbus status', or 'rcavahi status', or 'rcnetatalk' status.
You can see mostly all that happened using the 'logread' command right after a reboot, or, more comfortably, System->Utilities, Logs, System Log and looking near the end or searching for netatalk. Some services don't log to the system log, instead they use their own /var/log/<service>.log file.
Notice that the System Configuration "log" is generated at the end of the first boot step, and to regenerate it you need to hit the StartNow under Services->User. Before regenerating it, you will see no netatalk or avahi or dbus on it (look for the Services section -- 'rcall' from the command line), but after regenerating it you should see it:
root: netatalk running
root: avahi-daemon running
root: dbus-daemon running
(*) About aufs (another union file system)
there are three levels of folder unioning:
[root@DNS-323]# aufs.sh -l
aufs on / type aufs (rw,relatime,si=1a8e59c8)
this should be read from bottom up. At first, really-read-only, the original files from the firmware at /rootmnt/ro, so /rootmnt/ro/etc/init.d only contains the unmodified initscripts shipped with the firmware; if some of that files are modified, even its permissions, they will appear under /rootmnt/rw, which is read-write; modified files uses COW (Copy up On Writing); when finally a Alt-F folder appears on disk, the same thing happens (limitation -- only if the file or folder parents folder exists).
All these three folder structures are "amalgamated" together with complex rules to produce what you see under '/' and you should not directly manipulate them.
Ah, one more detail -- you will see in the System Log:
rcS: (14:40:07) loadsave_settings: loaded set_2017-10-23_14:33:00.tgz settings file.
That happens earlier on the boot, when no filesystem is still available. The settings archive contains a file with the name of initscripts that should be set to executable (executed on boot). As the Alt-F folder does not exists yet, it has no influence on it. initscripts files and its permissions for on-disk (Alt-F) installable packages are saved on disk, and should not appear under /rootmnt/ro or /rootmnt/rw.
If you have read so far, congratulations. I gave a full explanation because you gave a detailed report, thanks. You have now the basic knowledge to dig in your system, solve the issue and tell us what was happening wrong. Read also the "How to customise the firmware" wiki.