isteana: I'm not positive how ioFTPD handles timeouts. A really quick look at the EXEC module seems to indicate a script can run as long as it wants provided it outputs something at least every 2 minutes and the client is reading the output...
Do the scripts in question in fact print something while working? If not, then I suggest they should be modified to do so and see what happens. Removing the timeout just seems like a really bad idea, although I'm open to making it an option.
On the other hand clients like FlashFXP often terminate connections when the server appears unresponsive which may be as short as 1-2 minutes. I had to add status output to long running internal commands like file moving, etc to make the clients happy...
As an aside, it looks like the EXEC module doesn't terminate the started child processes under any condition but does close the stdin handle. This probably means the command will actually finish even if you are disconnected...
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