All versions of filezilla before 18.104.22.168 are not compatible with GnuTLS => 2.12.x.
As we don't have net-libs/gnutls <= 2.12.20 in portage, this affects all stable FileZilla versions.
This bug are explained on the FileZilla site (URL above). In short - due to GnuTLS design change from 2.12.x it yields FileZilla to stop FTPS/FTPES uploads after a few kBs are sent (connection timeout). 22.214.171.124 fixed this issue.
Steps to Reproduce:
1. Emerge stable FileZilla with recent GnuTLS
2. Try to upload to any TLS/SSL enabled FTP.
Bug 349442 and bug 449380 are still opened but shouldn't interfere with the stabilization of this package.
Unfortunately filezilla 3.6.0.x requires gnutls-3 to work correctly (somewhere in bug #431404 if I remember correctly), and this one is not getting stabled soon (it still has some open bugs against it)
Then another solution is probably backport/patch current version?
Unfortunately I can't help much with the patch, but found this: http://trac.filezilla-project.org/ticket/7808
Probably this could help to fix the issue in current stable version?
Security bug #479880 will start filezilla-3.7.2 stabilization (with or without support for FTPES/TLS), marking this bug obsolete then. Hoping gnutls-2.12 behaves fine with it, thanks for the report!