Hmm. That's weird for them to just brush you off like that, I've heard they usually have amazing customer service. Idk what to tell you but maybe ask around on Pirate. A lot more of those guys have Atlas t-cases over there than the people on WF.
I have heard of other people having the same problem but I have never experienced it. They are sometimes a pita to get in gear but mine has never popped out. I assume you checked for shifter clearances and the like? Beyond that, I haven't had to tweak anything.