mac texliveで埋め込まれないフォントがあるとき

原因はヒラギノフォントにあるようですね。
対応策は以下のリンクにあります。
http://blog.livedoor.jp/sphere496/archives/24679813.html

まとめ

sudo mkdir -p /usr/local/texlive/texmf-local/fonts/opentype/public/hiragino/
cd /usr/local/texlive/texmf-local/fonts/opentype/public/hiragino/
sudo ln -fs "/Library/Fonts/ヒラギノ明朝 Pro W3.otf" ./HiraMinPro-W3.otf
sudo ln -fs "/Library/Fonts/ヒラギノ明朝 Pro W6.otf" ./HiraMinPro-W6.otf
sudo ln -fs "/Library/Fonts/ヒラギノ丸ゴ Pro W4.otf" ./HiraMaruPro-W4.otf
sudo ln -fs "/Library/Fonts/ヒラギノ角ゴ Pro W3.otf" ./HiraKakuPro-W3.otf
sudo ln -fs "/Library/Fonts/ヒラギノ角ゴ Pro W6.otf" ./HiraKakuPro-W6.otf
sudo ln -fs "/Library/Fonts/ヒラギノ角ゴ Std W8.otf" ./HiraKakuStd-W8.otf
sudo mktexlsr

vim hiragino.map (つくる)

rml H HiraMinPro-W3
gbm H HiraKakuPro-W6
rmlv V HiraMinPro-W3
gbmv V HiraKakuPro-W6

hminr-h H HiraMinPro-W3.otf
hminr-v V HiraMinPro-W3.otf
hgothr-h H HiraKakuPro-W3.otf
hgothr-v V HiraKakuPro-W3.otf
hminb-h H HiraMinPro-W6.otf
hminb-v V HiraMinPro-W6.otf
hgothb-h H HiraKakuPro-W6.otf
hgothb-v V HiraKakuPro-W6.otf
hmgothr-h H HiraMaruPro-W4.otf
hmgothr-v V HiraMaruPro-W4.otf
hgotheb-h H HiraKakuStd-W8.otf
hgotheb-v V HiraKakuStd-W8.otf

ryumin-l H HiraMinPro-W3.otf
ryumin-l-v V HiraMinPro-W3.otf
gtbbb-m H HiraKakuPro-W3.otf
gtbbb-m-v V HiraKakuPro-W3.otf
futomin-b H HiraMinPro-W6.otf
futomin-b-v V HiraMinPro-W6.otf
futogo-b H HiraKakuPro-W6.otf
futogo-b-v V HiraKakuPro-W6.otf
jun101-l H HiraMaruPro-W4.otf
jun101-l-v V HiraMaruPro-W4.otf

これで、OMakefileに

DVIPDFMFLAGS = -f dlbase14.map -f cid-x.map -f hiragino.map

を追加すればOKです。