Hey Art. Starting with win7/w2k8 Microsoft made login sessions and the default service session protected from each other as a safety feature. I don't know if I could work around this or not using custom permissions, but for the moment the result is you can't send windows messages from user login sessions to the system session used by services. My guess is you are running ioFTPD as a system service (like you mentioned) but you are starting the bot from a user session...
You have 3 options. Start both from a user login session, use a tool like firedaemon to start both as a service since windrop doesn't know how to be a windows service, or use ioFTPD running as a service to start the bot. ioNiNJA I think has a way to do this but I've never used it.
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