I'm having this same issue with a SRX 5800. Started a ticket with JTAC but no resolution yet. I have disabled FTP ALG but the issue persists. We moved users from behind a redundant pair of Juniper 5200's and this issue did not exist. As soon as we moved our customers behind the SRX they could no longer perform FTP over explicit SSL.
We moved the customer back behind the 5200 and the connection works again so I know the block is taking place on the SRX.
JTAC had me start a traceoption and this is what I'm seeing:
Feb 24 22:31:26 22:31:25.1117349:CID-01:FPC-10IC-01:THREAD_ID-16:RT:FTP trace nat_ftp_line_break:1924
Feb 24 22:31:26 22:31:25.1117367:CID-01:FPC-10IC-01:THREAD_ID-16:RT:FTP line-breaker found, total length = 6, residual length = 0