i remember, that i had a similar issue in the past and i could solve it, by a systemwide terminal setting.
there is any option , where you can select, if the standard terminal profile opens the terminal as login terminal or not.
if you set this to login-type, then all the pathes and settings are inherited otherwise not
(i was fighting with some pathes which i've had in my login terminals, but not in terminals which were openend from gnome gui)
since that time i always set this option to login-type by default ;-)