None of the newly found aected moduli are blacklisted (cf. [24]). Based on this brief analysis, we conclude that the problem reported in the main body of this paper persists and that the 99.8% security level of 1024-bit RSA moduli is further reduced.

pp. 15 http://eprint.iacr.org/2012/064.pdf

They explicitly excluded the Debian/OpenSSL blacklisted keys from their sample before checking for shared factors.