Hi Liviu, It's strange that you're having this problem, I am as well. In my case, though I'm seeing it on the Windows SVN version. (I haven't updated on Linux for a while.) My Mac build of LyX is working just fine though.
I thought that I might have accidentally flipped one of the compile switches, but I haven't had much luck in finding which one. I also thought it might be due to an older version of fontspec, so I updated to the latest version this morning. Neither option fixed the problem. In your case, is it disabled for all documents or just new ones? Cheers, Rob