New Terminal At Folder service in El Capitan doesn't use my Terminal profile settings
After launching Terminal.app the active profile of the shell  window is determined by the settings chosen in: Preferences > General > On startup open...

The profile of the next Terminal window opened or the one launched by Services -> New Terminal at Folder uses a default profile which can be configured here: Preferences > Profiles > Text: choose a profile in the left pane and hit the default button at the bottom.