There seem to be a number of SSL related oddities between flashfxp and drftpd (and probably other clients), it is worth noting that the 2.0 branches of drftpd do not use an openssl inplementation at all, so this issue may infact arise from java itself or the ssl libraries used (or in combination with each other).
Generally the only time i experience negotiation failures during connection is when my personal internet connection is under fairly heavy use (such as using full or close-to-full upstream bandwidth), i have always thought that this may be related to the time (lag) taken for the negotiation to finalize being too long, but thats nothing more than a guess really.
For those willing, you may try testing the new 2.1 branch (non-stable) of drftpd to see if the ssl lib changes effect this issue.
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