This question is an old post, so I doubt my reply is still relevant, but if not, someone else might need it instead.
I had this problem too, although there may be more than one cause for the dastardly "Quick Setup" effect.
When I first connected to the ATA web interface, at firmware version 1.0.2(006), all menus were present and correct. Then I reset to factory defaults (at least, I think that's what I did) and the menus suddenly screwed up. For instance, if I clicked "Administration", it showed one Administration option, but no menu tree structure in the left-hand panel. The right-hand panel was titled "Quick Setup", even though it was the Administration menu. Rebooting my PC, the ATA and even swapping browsers made no difference. It was working fine, and then it wasn't. Nothing I could do would bring it back, so this was messed up ATA firmware.
The fix to this problem is to do a firmware upgrade, but ironically, the Firmware Upgrade option is under Administration, which is all messed up. You can still do the upgrade, but not using the Administration menu. Here's how:
First, choose a general-purpose firmware version that isn't one you want to upgrade to (I chose 1.3.3, for example). Download the .zip file for this from Cisco's website. Open or unpack it to see what the filename of the firmware image is. Then put that filename into your favourite search engine. In my case, this was "spa112_spa122_1.3.3_015.bin". The search should return a webpage having a download link to the firmware image. Right-click the link, copy it and paste it into a text editor, such as Wordpad, Notepad, Gedit, etc. In my case, the result was this:
http://c-talk.weebly.com/uploads/5/3/1/5/5315472/spa112_spa122_1.3.3_015.bin
(Now that's not a Cisco website, but what the heck!)
Back at the ATA web interface, click on the "Voice" menu, and paste your URL (whatever was returned by your search) into the Upgrade_Rule field. Also under the Voice menu, ensure that firmware upgrades are enabled, which is the default. Then save the settings.
(At this point, my memory fades a little. I don't recall whether an ATA reboot was required to start off the upgrade, so bear that in mind. I've a feeling it just starts automatically. I was doing this work off the internet, so I briefly connected the ATA to my internet-connected switch to allow the upgrade to start.)
The ATA LED's start blinking and after a moment, the Network LED starts flashing rapidly as the firmware image downloads. When it stops flashing rapidly, you can disconnect the network cable and let the upgrade proceed on its own. There will be more LED flashing as the upgrade completes and finally, the ATA reboots. You will now be at your mid-way firmware version (1.3.3 in my case).
You've just downloaded and installed untrusted firmware into your ATA, so the next thing is to upgrade to another, trusted version, such as the latest from Cisco. Your menus should be restored to normal now though, so just do the second upgrade in the usual way. This gets you out of a hole.
[I spent days looking for a way to do this, poking around in HTML, but after skimming through the Provisioning Guide, the answer was obvious.]
