A work-around that may work for you is to place the old emulateapj.cls
and revtex4.cls in the same directory as your latex document. That
should be higher in the hierarchy so they override the installed
versions.

I haven't had anyone in my department (Penn State Astronomy) have any
problems with the latest emulateapj. They've all been really happy with
it here to my knowledge.

-- 
incompatible version of emulateapj with revtex4-1
https://bugs.launchpad.net/bugs/609147
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