Mozilla's list also includes distrusted certificates, so you need to be careful to leave them out when generating the PEM-encoded format. In fact, I'd strongly recommend using Adam Langley's excellent extract-nss-root-certs tool [2] which takes care of the subtle details for you.
And, if you are willing to trust me, you can download my pre-generated PEM-encoded cacerts file from a month or so ago [3].
[1] https://mxr.mozilla.org/mozilla/source/security/nss/lib/ckfw...
[2] https://github.com/agl/extract-nss-root-certs
[3] https://github.com/downloads/tav/ampify/distfile.cacerts-201...