My only guess is it's possibly related to removing the sha256 algos, but... that was even before I started doing the compilers job for scrypt.
Not sure what to do other than general hints along the lines of "start with a clean tree, CFLAGS="-whatever" ./configure; make"
Hrrrm... I guess you could revert the sha256 removal or drop the new scrypt.c into Tenebrix-miner and see if that also causes the same issues.
There is no scrypt.c in your latest released source of 1.0.2... I'm looking at the tar.gz and it's missing it.
edit: It works just popping scrypt.c in, I'm getting 3.87kh/s now per core