I found this post as I started having the same pop-up error yesterday after I installed and configured Netatalk. I have a slightly different set-up.
Linux server running Netatalk 3.0.2
Ethernet connection to the server.
iMac 10.8.2
While I copy or read data from the server, there is no pop-up. As soon as the network connection is idle the pop-ups start.
I didn't have any pop-ups for quite a while. I think this is because mdworker (Spotlight) was indexing my shared folder on the server. So I stopped Spotlight from indexing the two shared folders on the server. Now I see mdworker giving an error.
At the moment I have VLC playing something in the background. VLC (probably any other app reading from the server) stops the OSX idle and so stops the dialog box from showing up.
From the console:
Feb 17 11:42:54 VLC[2773]: kIOPMAssertionTypePreventUserIdleSystemSleep
Feb 17 11:46:32 mdworker[3221]: Unable to talk to lsboxd
Feb 17 11:46:32 mdworker[3220]: Unable to talk to lsboxd
Feb 17 11:46:33 kernel[0]: Sandbox: sandboxd(3222) deny mach-lookup com.apple.coresymbolicationd
Feb 17 11:46:33 sandboxd[3222] ([3221]): mdworker(3221) deny mach-lookup com.apple.ls.boxd
Feb 17 11:46:33 sandboxd[3222] ([3220]): mdworker(3220) deny mach-lookup com.apple.ls.boxd
Feb 17 11:47:33 mdworker[3228]: Unable to talk to lsboxd
Feb 17 11:47:33 mdworker[3229]: Unable to talk to lsboxd
Feb 17 11:47:33 sandboxd[3230] ([3228]): mdworker(3228) deny mach-lookup com.apple.ls.boxd
Feb 17 11:47:33 sandboxd[3230] ([3229]): mdworker(3229) deny mach-lookup com.apple.ls.boxd
Feb 17 11:47:34 kernel[0]: Sandbox: sandboxd(3230) deny mach-lookup com.apple.coresymbolicationd
Feb 17 11:49:34 mdworker[3237]: Unable to talk to lsboxd
Feb 17 11:49:34 mdworker[3236]: Unable to talk to lsboxd
Feb 17 11:49:34 sandboxd[3238] ([3237]): mdworker(3237) deny mach-lookup com.apple.ls.boxd
Feb 17 11:49:34 sandboxd[3238] ([3236]): mdworker(3236) deny mach-lookup com.apple.ls.boxd
Feb 17 11:49:34 kernel[0]: Sandbox: sandboxd(3238) deny mach-lookup com.apple.coresymbolicationd
I suspect that the OS does some sort of system sleep for the network. This causes a temporary disconnect to the server (or connected drive) that then causes the dialog box to pop-up.
Are you getting the same messages in the console??