I had the same problem with dkms being unable to build my nvidia driver.
I found that the problem for me was the kernel-headers package.

I am running 2.6.25-2-386.  When I installed the linux-
headers-2.6.25-2-386 package it created the proper /usr/src/linux-
headers-2.6.25-2-386 directory tree.  That directory has number of
symlinks, for example:

drivers -> ../linux-headers-2.6.25-2/drivers

However, my OS did not have a /usr/src/linux-headers-2.6.25-2.  Instead
I have a /usr/src/linux-ports-headers-2.6.25-2.

Thus every reference in /usr/src/linux-headers-2.6.25-2-386 was pointing
to nowhere.

I resolved this manually by creating a symlink /usr/src/linux-
headers-2.6.25-2 -> /usr/src/linux-ports-headers-2.6.25-2 and this fixed
my problem.  DKMS will now properly build the nvidia (and who knows what
other) driver and I am back up and running.

I don't know if this is an ubuntu issue or a package maintainer issue or
a kernel issue.  My manual fix is probably not the right thing to do,
but I had to get back up and working. YMMV

-- 
Upgrade to Ubuntu 8.10 Alpha 3 stops Nvidia driver working
https://bugs.launchpad.net/bugs/252160
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