I don't know of anything extra you need to do ... I've been compiling kernels using the source from the kernel.org and patches from Kolivas, doing it about the same way: copying over my last config, doing make oldconfig, make menuconfig, make bzImage, etc ...
Is it possible that the old config had some things relative to vl kernel patches (aufs, squashfs and lzma) that resulted in borkage when compiling a kernel without those patches?
Just took a peek in the kernel build file for the VL 126.96.36.199 kernel ... saw that squashfs is built outside the kernel, and the script removes it from .config before configuring
There was a how-to on compiling kernels here, but I think it's one of the topics which disappeared.