This isn't a configurable setting.
However I added a 60 second timeout for establishing a data socket connection, this should resolve the problem you're experiencing, you can test these changes in the
latest beta
What I suspect is happening is that the data connection times out or takes longer than 2 minutes, after 2 minutes of waiting for a reply FlashFXP will terminate the connection. By lowering the connection timeout to less than 2 minutes we should be able to handle these situations better and instead of the control connection being lost FlashFXP can just try again with a new port combination.
I am very curious to see how these changes work for you.