1) Update make.conf:
# emerge app-portage/cpuinfo2cpuflags
Run:
# cpuinfo2cpuflags
Then update your CPU_FLAGS_X86 (cause I think that there are also mmxext (native in Athlon but renamed in Intel's cpu, such as sse3 are named PNI ("Prescott new Instructions))
Then You're core2 is precedent of "Penryn" family that supports also sse4.1
If you want try also
grep sse4 /proc/cpuinfo
to be sure that there aren't also sse4.1 streaming simd extensions.
For Other questions, mmm I use the "Stable branch" of portage.