Did you use the debian package linux-header-2.6.32.6 or you use knoppix package ? There will be some difference between debian package verses knoppix (custom) package - because knoppix is patched with aufs2. Unless you are compiling file system drivers, otherwise it should not matter. What are you trying to compile ?

If you have exhausted everything, you can always go to www.kernel.org to download the kernel source. You can't use the kernel you compiled from www.kernel.org, but the header files there should be good - as long as you are not compiling file system drivers.