Several build steps modify auto.conf which may then have a knock-on effect on later build steps. We should restore the auto.conf to the default state, as created by the CreateAutoConf step, at the end of buildsteps which modify it in order to ensure the environment for the build is as expected. Such a change was already made to RunSanityTests in order to resolve issues in the jethro build: http://git.yoctoproject.org/clean/cgit.cgi/yocto-autobuilder/commit/?id=e675e6a7e8d06dcd0141394f329b74c2f5da21fa but this should be generalised and used more widely post M1.
The change to RunSanityTests had to be reverted because it was causing exceptions on several of the builders on the YP cluster: http://git.yoctoproject.org/clean/cgit.cgi/yocto-autobuilder/commit/?id=b5007ccf74e6f31c419a0b6b06f467ab9c9379b7
Effectively resolved by the new infrastructure architecture of helper scripts (yocto-autobuilder-helper) with a more recent buildbot with minimal configuration (yocto-autobuilder2).