I'm in the middle of an update, so the sources from SVN couldn't be ready for a direct build. Input.inc has been reworked a little bit, so now it is divided in two files (the first one in nds/ directory, the second one in the nds/arm9), but I haven't uploaded the latest changes to SVN yet.

I'm afraid that your setup could be wrong, because sometimes the RTL is updated according to changes in the compiler. For example, often the linker script and the crt0 are updated in devkitARM at the same time, but in freepascal the linker script is hard coded in the compiler itself. So rebuilding the rtl and the nds library is not always enough. A complete rebuild should be the right way