Can a server be prone to this glitch?

Recurring prob with multiple SEs

[millie]

5 sites now! Our sites seem to be being indexed with and without www. This is becoming an increasing problem.

With one site there were inbound links to domain.com so it seemed clear what the problem was. But with the others there doesn't seem to be an obvious reason.

Main engines that seem to index both ways are Google, Inktomi and ATW.

The sites are set up as domain.com and there is an alias set up in the DNS that allows people to access the domain using the www.

I can set up 301s on every site no problem but do you think there's something more integral to the server (Windows 2000) that I should be looking at? Some setup / config issue perhaps?

[bakedjake]

But with the others there doesn't seem to be an obvious reason.

Yes there is, you mentioned it two lines down:

The sites are set up as domain.com and there is an alias set up in the DNS that allows people to access the domain using the www.

Pick one, and stick with it. Kill the other from your DNS, or alternatively, leave those 301 redirects up that you've put in. That's probably the better solution anyways, in case there are people linking to the wrong one. ;-)