If it's the identical ioFTPD.ini and Hosts.Rules files (it's WAY too easy to mess up ioFTPD.ini file in some subtle way) and everything else the same except the executable then I'm baffled since you can talk to it locally so you know it's running in both cases...
If you drop both version into the same system dir and run one then the other and the newer fails, but the older works, then try reverting to a plain generic 6.3.5 file or even a 6.2.1 file just to rule out new features like something wierd going on with immune hosts, users, etc.
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