pythonstartup ignored?

[Gordon Blackshields]

Using Anaconda under OSX, I have a startup script that, for the most part, ensures environmental variables are present in os.environ. This is set as the pythonstartup file for both python and ipython consoles. When interactively opening a new console, everything seems ok. However, when executing a script (in a new console each time), the setting seems to be ignored. Is this expected behaviour?