I have created a custom master page for my site, but when I have set it as the site's master page the changes I have made to default.aspx no longer seem to be working.

I have changed the site's default.aspx page with a small bit of custom JavaScript, this works fine when using the v4.master, but as soon as I switch to the custom master page it stops working as if it's not using the default.aspx I have altered.

Any idea what could be causing this?