Aha! I figured it out. I’d forgotten that OS X changed the way environment variables are set globally for GUI apps. In 10.7 you used ~/.MacOSX/environment.plist, but in 10.8 onwards you use /etc/launchd.conf.
I thought they killed environment.plist in 10.7? Regardless, it is indeed gone, and you need to use one of the functioning launchd files. Just don't rely on the man page for accurate information.
Of course, I edited the wrong one, which had no effect on BibDesk, but everything still worked at the command line because that uses a different initialisation mechanism. I fixed the TEXMF* variables in launchd.conf, rebooted, and now everything is working again.
Glad you figured it out. This is precisely why I added logging of TEX* envvars for the TeX preview last night, since I've had bad experiences with clever users setting various path variables (which play hob with the TeX Live Utility program that I maintain). With that in mind, I strongly recommend that users DO NOT SET ENVIRONMENT VARIABLES LIKE THIS! Problems that arise from this technique are an absolute nightmare to debug, since users invariably a) forget that they edited these files and b) override them in the shell, so things "work" in Terminal.
Adam
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