I'm using dylan for my yocto checkout (not oe-core standalone, since
this is a yocto list/question),

My build shows:

meta
meta-yocto
meta-yocto-bsp    = "dylan:3dc4505f0e744177ae4ddff1e1ce8b31b95dfaa6"
meta-ti           = "master:c14c386946e1ea341faeea292580e37d538d645d"
meta-alphalem     = "master:a5c0e8ff51297a4090cd47d669b4fc9c94696908"
meta-alphalem-bsp = "master:56086e4dc618e975c9a46491793041f0d18e47a2"

Mike indicated that he was using dylan for meta-ti, but that doesn't
make a difference either, since for our purposed. It's kernel.bbclass
and the yocto kernel processing that matters.

In meta-alphalem-bsp, I have linux-mainline_3.2.bbappend, with the
following content:

> cat linux-mainline_3.2.bbappend
FILESEXTRAPATHS_prepend := "${THISDIR}/${PN}-3.2:"

inherit kernel
require recipes-kernel/linux/linux-yocto.inc

COMPATIBLE_MACHINE = "(beagleboard)"

SRC_URI_append = " file://defconfig"
SRC_URI_append = " file://my_frag.cfg"

And I added a fragment which has:

> cat my_frag.cfg
CONFIG_WATCHDOG_NOWAYOUT=y
CONFIG_NTFS_FS=y
CONFIG_NTFS_RW=y

When both are applied to the kernel build, we should see CONFIG_NTFS_FS
transition from =m to =y:

> grep CONFIG_NTFS_FS *
defconfig:CONFIG_NTFS_FS=m
my_frag.cfg:CONFIG_NTFS_FS=y

After invoking linux-mainline's configure task, I see the following:

> grep CONFIG_NTFS_FS linux-beagleboard-standard-build/.config
CONFIG_NTFS_FS=y

And other elements of the defconfig and fragment are properly applied
to the configuration phase.

I'm also seeing good results on master, which means that I'm at a
standstill to reproduce any problems.

Diego: can you confirm for me what triggers you are seeing that shows
the defconfig and fragment are not used. I assume the config options
are not present, but I just want to be sure.