What's the specific timeout message you're getting? Also, have you tried setting the debug level to something higher? According to the Net::Cmd docs (since Net::FTP inherits from Net::Cmd), the debug level may be set to more than 1, and different packages give different response.
Update: You might also try using a network sniffer (if that's allowed on your network) to see what's actually being passed between your Linux and Windows box. Ethereal comes installed on a lot of linux distros, and has a pretty nice GUI, or, if you prefer the command line, you can use tcpdump.
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Error executing run mode 'send_file': Cannot connect to host: Net::FTP: connect: timeout at /home/domains/xxx/www.xxx.com/aa/system/modules//FTP.pm line 16.
at /home/domains/xxx/www.xxx.com/aa/index.cgi line 20
I don't know how to se the result of the debug information!
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