I have found out that when creating a plot with time format in the x-axis,
set timefmt "%s"
set xdata time
there is a difference in the use of the column specifier.
There is no problem by using the full form.
plot "timedata1" using ($1):($2), "timedata2" using ($1):($3) axes x1y2
however when using as
plot "timedata1" using 1:2, "timedata2" using 1:3 axes x1y2
the time data is not properly interpreted.
I noticed that when the timedata1 and timedata2 files are the same then
there is no problem at all,