There were a few problems, related to the RTAI patching and related to the make-kpkg package.
The stranger problem (related to make-kpkg) is that the new kernel didn't show an usplash, to fix that I've been told this is a temporary fix:
put this script (post-install) in the kernelsource/debian/ directory:
#!/bin/bash
cd "$IMAGE_TOP/lib/modules/$version"
mkdir initrd
if [ -f kernel/drivers/video/vesafb.ko ]; then
ln kernel/drivers/video/vesafb.ko initrd
fi
chmod +x post-install
this way the splash will work as expected.