The "jerk" you speak of is likely the screen area being cleared before
being redrawn. As far as I know, this can't be avoided, at least not
using the x11 terminal. If you want, you could get your hands dirty
and add double-buffering, where the graph is first drawn on an bitmap,
then blitted to the screen, rather than directly onto the screen.
A shorter period between plots will result only in more rapid
flickering. As for the slower plotting with longer data files, well,
that's the nature of taking data from the end of files without a
well-defined record length. A possible solution: since gnuplot is
being controlled by a (continuously running) perl script, why not keep
the last 60 seconds of data in an array in your script, then plot
using inline data, where gnuplot looks for data from stdin? See `help
special-filenames` for details.
I've never done anything like this. That said, you could use the
`tkcanvas` terminal to generate Tk canvas widget commands. Or you
could have gnuplot plot to a bitmap file using (e.g.) the `png`
terminal, which file you GUI might then be able to display. Both of
these solutions, I think, effectively implement double-buffering, so
you get rid of the "jerk" as well.