This code hasn't been changed since v1.4, as for v1.2 no telling. Perhaps we broke something or the settings have changed. It's hard to say based on what you provided us.
What I need is a copy of the status log from both v1.2 and v2.0. By comparing the two logs I can determine what settings need to be set.
As far as passive mode goes, the "Use Passive mode" only effect listing and ftp transfers. not FXP.
To adjust passive mode for FXP transfers you must use "Alternative FXP" exclusively. When enabling this, you need to insure you only enable it for 1 of the sites, the one that needs it, otherwise you cancel each other out.
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