That's because the start up scripts are evaluated after macroscripts as described in the link Monster provided. You should put your start up scripts in a local folder on your computer and then add that path to the Customize > Configure System Paths > 3rd party tab dialog and restart max. Your start up script will then load…
You can add macros into that directory if you would like to but be careful if your doing this for a team of artists and the folder is on a shared network. If another artist right clicks the macroscript in the customize dialog and chooses "Edit Macrosript File" they could potentially change the one on the network and not…