I recently downloaded the latest version of Atlantis and I'm quite happy with it, as always. BUT...every time I launch the program I get the dialog box asking me if I want the new toolbar to supercede the old one. The first couple times I clicked "no", but then when it kept re-appearing I clicked "yes". OK, change the toolbar, just make the box go away. No luck. It comes back every time. And every time it comes back I hit "enter", which is "yes", the box disappears, the program opens. At this point I can not remember what the old toolbar looked like or whether I'm getting the new or the old. I just want the BOX to go away so I can open the program.
The home folder of your Atlantis (as a rule, "C:\Program Files\Atlantis\") should contain the "Atlantis.ats" file (Atlantis Toolbar Settings). Is this file locked in some way (for example, has the "read-only" attribute)?
Maybe you are using Atlantis with a special command-line telling Atlantis to never save its settings on close. What is the command-line associated with the Desktop shortcut of your Atlantis?