Site Collection created from the Team Site template and Wondering where the Master Page settings are ?
To solve this problem we had to enable the "Office SharePoint Server Publishing Infrastructure" feature at the site collection level. Once this had been done the "Master page" link appears and you can set the alternate CSS as you wish.
I'm reliably informed that the reason it isn’t there is that it wouldn’t normally be available on a WSS only infrastructure (we were running MOSS, not WSS) so the team site template has no dependency on it. So if you need this functionality within MOSS and you've created the site collection from the team site template, make sure to enable the "Office SharePoint Server Publishing Infrastructure" feature at the site collection level.
UPDATE 25-04-07: Turns out that the "Navigation" link under the "Look and Feel" section of the site settings page is also affected by the presence of this feature too - I wonder what else it affects ?!