I don't know, I separately build Arcade and MESS binaries, that is the only modification I made in the makefile provided in the official MAMEDEV archive: the OSX is the latest, the command line tool is the latest (Xcode suite not installed, only the command line tools), SDL2 framework is the latest, macports binaries and distribution are also the latest
I can try to compile the omnicomprensive MAME binary (Arcade+Home) leaving makefile untouched and I will let you know if this issue persist.