No. It's not the kernel.

When you compile a .c or .cc -file, the output is by default an '.o' file - aka 'object file'.
Since kernel 2.6 the kernel-object-files are named '.ko'.

So the kernel is looking for the correct .ko -file, but sndconfig is looking for the wrong one.

I don't know whether a new sound-configuration script is generated for linux 2.6 and how it is called. Perhaps you don't need it anymore?

I don't know whether changing the sndconfig-tool to use '.ko' instead of '.o' is:
- possible (it's a binary, you would need to find the sources)
- helpful at all.