That error message is actually coming from the fglrx build script
(make.sh):

Walking through it's logic, it is getting the 2.6.28 from your command
line.

It then checks for the existence of the directory 
/lib/modules/2.6.28/build/include
If that directory doesn't exist it uses /usr/src/linux/include

Once it figures out what directory it is using, it is checking for
./linux/utsrelease.h

That's the file it's not able to find and match to UTS_RELEASE to
2.6.28, it isn't going to work.

-------

Hopefully that makes sense.  You'll need to adjust your custom build to
match that situation.  I'm closing this bug as "Won't Fix" because it's
in the AMD portion of make.sh, and there is nothing that we will be
doing other than redistributing it.  Making modifications makes
maintenance harder from release to release, so it's best to adapt around
it instead.

** Changed in: fglrx-installer (Ubuntu)
Sourcepackagename: dkms => fglrx-installer
   Importance: Undecided => Wishlist
       Status: New => Won't Fix

-- 
dkms fails to build fglrx for new kernel
https://bugs.launchpad.net/bugs/320986
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