I'm not sure if everyone is getting this as we may be using different versions of Atlas and AtlasLoot. But for the versions I am using I was getting a pop-up everytime I logged into a character coming from the AtlasLoot add-on telling me that the version of Atlas is older than the version of AtlasLoot and that I should go to their website to update. Since I was not sure if I could find the correct version of Atlas I decided to just change the code to remove the box.
Clicking two boxes every time I log into a character was getting really annoying. I've included a download to download my edited version below. Leave a comment if this was helpful.
PS: I also included in the folder an edited version of EasyCopy. EasyCopy is an add-on that was included in the WoW folder if you downloaded it off of Nostalrius' website. If would fade-in + fade-out some text every time you logged into a character as well. The edited version that I have included has removed that, enjoy!
Link to Files: http://www.mediafire.com/download/tg7ameaglbnj4le/Atlas+%2B+AtlasLoot.rar
I also have a little before and after video that I made to show what I am talking about.
Link to Video: https://www.youtube.com/watch?v=L5Db_pPMMNs
If this ends up being a widespread issue maybe a sticky is in order.