Did you try looking at the owner of the user's pub_html directory?
You can do that with the next command:
ls -la /home/username
The pub_html folder should be owned by username.users
I did try adding a user with the 040 control panel, and the user was added, but the directory wasn't owned by the user. To be honest I'm not 100% sure because my vmware machine did not report back after creating the user, so YMMV.
Also did you try my suggestion I posted earlier to change the owner of the directory?
Another suggestion is to upgrade to a later version because 0.4.0 was the first 0.4.x version and 0.4.2 may be better.