Description of problem: In /usr/include/linux directory there are includes for kernel 2.4.20 !! (look to the /usr/include/linux/version.h file) but the system works on 2.6.5 kernel.
those headers only describe the interface between the kernel and userspace, the "version" is irrelevant and no app should use it; it just needs to be there as "something".
Maybe you're right but some programs need the file version.h to compile. They look for it in /usr/src/linux-x.y.z-*/include/linux but it isn't there so I thought that /usr/include/linux/version.h is the same. Maybe it's a bug in kernel-source package... If not - what should I do? - I can't compile my ADSL modem driver because I always get the message: "error: kernel-sources version is different from the current kernel!" hmm...
well kernel modules cnanot use /usr/include/<anything> really. Sounds like a kernel module with a misdesigned makefile (eg what they do may have worked in Red Hat Linux 6.2 but not afterwards). I would recommend you to read the files in the Documentation/kbuild/ directory about how to build external kernel modules.