I'm also hitting this problem.  Obviously the correct solution is to
move nis to use upstart and then make autofs depend on nis being up.  In
the interim, I've modified autofs.conf to wait for the rc process to
finish:

  start on (filesystem 
        and net-device-up IFACE!=lo 
        and stopped rc RUNLEVEL=[2345]) 
  stop on runlevel[!2345]

-- 
NIS-based autofs maps don't load on startup
https://bugs.launchpad.net/bugs/570513
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