Yes perhaps you could have that ini setting being shown under session - on transfer complete, so you could enable and disable it whenever you would like to use it (being enabled as default) ?
Also maybe you could make the help file a bit more easier for us to understand.
[run]
app <full\path\to\exe> This command will be executed upon a sucessful file transfer.
param <params> any params you need to pass, use the %f macro to pass the filename
show=1 (0=hidden 1=visible); show application window has two values 0=hidden 1=visible
doesnt say me much, ive tried many combinations of
[run]
app C:\Documents and Settings\Administrator\SendTo\yes2.bat
param %f
show=1
and none works.