Is AFP of any value to non-ancient devices

It turned out that the issue was indeed different UIDs though the usernames were the same.

From the Apple Support Communities link:

borbye:

The first user that is established on an OSX disc is given UID number 501. Normally next user is given UID 502. In my case I could not import my existing user during first run with my new MB Air. Had to establish a testuser and later import my existing user. It turned out that the testuser was giver UID 501 and my existing user was given UID 502. Result was the existing users on the two macs are not the same even thoug the username and login is identical..

I tried what was suggested in the support thread and screwed up my entire system - as he had clearly warned.

borbye:

Check your users in systemprefs -> accounts - open the lock and right click on user -> choose advanced options.

NB: Dont even think you can just change the UID for the user and it will work..... If some more advanced users have a script to change the UID for all files in a home folder, please let us know..

The workaround suggested at the thread didn't quite work for me. But I am not sure if I missed any steps. So you can try this at your own risk.

one51mac:

borbye is correct that this will remedy the problem but there is a way to do it and have your account work. after changing the user UID and group UID to 501 you will have to restart. then when you log on your home folder will still be your default but you will not have any access. Since you are still an admin you can change that. right click on the home folder and select get info click arrow for sharing and permissions. Your old UID account will show up as _unknown delete this user and add your user to it giving yourself read and write privilege. click on the cog on the bottom and select apply to enclosed items. A warning box will appear stating that this process cannot be undone do you wish to proceed? click yes and a status bar will come up. once the bar is gone the process is complete. since you didn't have access to your home folder you cannot save your settings, this is a good thing since your account will not look remotely the same as yours most likely. all you have to do now is logout and then back in. Your account will look as it did before the change with all the access settings and so forth as before the change... minus some permissions due to the overwrite. It's a minor repair to the permissions to some shares considering you will be able to now move files to and these shares without the permissions alert that only creates a 4kb file instead of the real thing. Takes 5 minutes at most. Have fun.

Ended up doing a fresh install and created a user with the same username as the first one. It took a lot of time to backup and restore all the data but finally I am back on track.

I, too, find this a pain with my QNAP box. FYI the firmware has now been updated to 3.6.0 released just a few days ago, and there is some noticeable improvement with the update. However, you may consider using the iSCSI feature among the QNAP settings to make the file shares appear as a hard drive showing up on your desktop for better speed. I've noticed iSCSI works better IMO if your connection to the QNAP is hardwired throughout and not wireless in any way; wireless iSCSI works, just not as fast in my experience.