There's no reason for vanilla-kernel working and gentoo-sources don't.
The main reason is that:
a) The filesystem in gentoo-sources you selected it as a module instead
of built into the kernel, and in vanilla-kernel you did right or maybe
it was selected.
b) The IDE chipset driver or IDE hard drive driver wasn't selected in
gentoo-sources, as they were in vanilla-kernel.
The .config file itself would't say lots of things, but it would be more
useful a diff between two .config files (the one that had gentoo-sources
and the vanilla-sources), and maybe we could check out what is now
selected that wasn't before.
Anyway, if it works now it's ok.
Bye,
Rafael Fernández López.
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