Unfortunately no one can be told what fun_plug is - you have to see it for yourself.
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I have funplug installed, mediatomb installed and a configuration setup for smb. I have two scripts that I want to run on boot, one that changes the current smb configuration when you boot to my custom config and the other to start mediatomb(not the funplug one) I thought by putting the scripts in the ffp/start and giving them execute privileges, it would auto start but that doesn't seem to be working. Am I doing something wrong or what do i have to do to get them to run on boot?
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check which start script is the last one to go off (you can check this in the ffp.log) and put a line in that start script that triggers your own script. Maybe smb is not running yet in your first situation.
Maybe you can find some more info or error codes in the ffp.log
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