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The BSP that is currently supported for the Galileo is the version 0.7.5 (the one that is in the download center for the Galileo https://communities.intel.com/docs/DOC-22226 ). I do know that other users have already built the one in the download center for the Quark (https://downloadcenter.intel.com/Detail_Desc.aspx?DwnldID=23197 ), there are a couple of post about that, but let me try to build it myself if I get a different result from the one you are getting I would post it here.
As far as I can see, quark-init recipe provides a mean to autoload drivers upon board is booted. I can't recall whether it was called the same in 0.9.0, but the same functionality was there for sure - I was using it to stop autoloading wi-fi drivers I don't need.
It's actually included into both image-full-galileo and image-spi-galileo image recipes, so such a difference you see can only be explaind by the fact that your custom "full" recipe you refer to is not derived from image-full-galileo one. I guess you may have created it based on some previous BSP version and after they've reworked stuff in 1.0.0 or 0.9.0 (0.8.0 was closer to 0.7.5 AFAIU) - that no longer works as intended.
The best way to fix that IMHO would be to create your custom recipe anew, based on the image-full-galileo one.