Two possibilities come to mind:

(1) It's not really gone...

Are there any other extensions that could be causing this?

Tools > Add-ons > Extensions category

(2) Firefox is failing to save preference changes at shut-down...

Assuming Firefox isn't crashing at shutdown, it could be a problem with a settings file. See How to fix preferences that won't save.

What is the home page?

Is that the about:home or the about:newtab page or a different web page?