I'm using kernel with config in /proc/config.gz file. make command while building new kernel automatically invokes 'make silentoldconfig' if /usr/src/linux/ contains .config from previous (current) kernel. Normally 'silentoldconfig' should automatically update kernel config file making default choice. Currently it works exactly as 'oldconfig': asking user about his choice for each added config item. This issue appeared rather long ago and is valid for all tested gentoo-sources-2.6.3x kernels.
"Make silentoldconfig works exactly the same way as oldconfig does, but it does not print anything to the screen, unless it needs to ask a question about a new configuration option." http://www.linuxtopia.org/online_books/linux_kernel/kernel_configuration/ch07s03.html