I had a similar issue with an user I was supporting (our IT
does not "support" Macs, and has minimal experience, but as the Unix guy I got to support this user).
The user was complaining about differences between xterm and
default terminal. One difference was emacs would start in
separate window on one (I think xterm) and in non-windowed mode in other. Setting $DISPLAY in terminal did not change
situation.
I could not figure out differences re where the two were getting default paths, etc (I think one was running tcsh and the other just csh, no idea why) so eventually just added to .cshrc a line explicitly adding any dirs occuring only in one term app's path (figuring dups in path are relatively harmless, and assuming order should matter little). At that point neither would open a new window.
Anyway, I can't explain above or the following, but by aliasing emacs to something like /Applications/Emacs/.../Emacs
(forget the exact path, but there was an Emacs with capital
E file in directory one or two above the one with the emacs
executable found by 'which' command), the command would
always open X emacs window.