I think I'm having the same problem as this
I've had the same problem using versions 2.9.2 and 3.0.1 (I reverted back to 2.9.2 at some point). I'm running this on xubuntu and everything generally seems to be working fine.
I used the instructions at http://codex.wordpress.org/Creating_a_Static_Front_Page to set up my static page at <lan ip>/wordpress and my blog page at <lan ip>/wordpress/news.
When I use /%postname% as my permalinks structure I can access yearly, monthly and daily archives as expected at <lan ip>/wordpress/<year>, <lan ip>/wordpress/<year>/<month> and <lan ip>/wordpress/<year>/<month>/<day>.
Unfortunately I would like to set the permalink structure to /news/%postname% and this results in the yearly archive (eg <lan ip>/wordpress/news/2010) displaying the theme's index.php. The monthly and daily archives still work as expected.
I've tried a couple of themes, including the default theme, but the problem remains. I only started using wordpress a week ago and I don't really know what to try next.
Is anybody able to shed any light on this or suggest anything I can try to fix this?
Thanks in advance.