net-ftp/filezilla should check with gentoo global certificate file /etc/ssl/certs/ca-certificates.crt. It seems to be looking for ca file in default path.
After checking http://wiki.filezilla-project.org/SSL/TLS#Client_Setup this looks like a feature request for upstream, they seem to use a XML file stored in ~/.filezilla, and not standard .crt files?
Correct me if I'm wrong though, I don't use FTPS, so I never had this problem
Hmmm, certainly can remember manually setting up the certificates path. And it seems that once they switched from openssl to gnutls they changed thier certificate storage.