Currently this isn't a user configurable setting however I think that this is a great suggestion and we could possibly add this to future versions of FlashFXP.
I do see some challenges with incorporating this type of behavior change. Specifically the current logic forces the current folder to be selected in the tree-view at all times, however to prevent the auto-expanding of the folders we would need to bypass the folder selection during a transfer which is somewhat trivial, what then becomes rather complicated is that if the tree-view isn't selected and the user selects it, on tree-view focus we need to then select the current folder and when the current folder no longer matches the selected folder in the tree-view we would need to determine if this selection needs to be removed, otherwise the user is going to think they're in one location as indicated by the selection while the file list-view is displaying a completely different folder.
Perhaps a better idea might be to simply not update the local/remote browser during a queue transfer and have the browsers remain in the current directory, that way the location doesn't change at all while processing the transfer queue. This is something that I've considered in the past and planned to implement into v5.0.
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