This is a result of the fact that OpenGL uses variables of type single, ~8 digits of precision, while gnuplot uses doubles.

This is a duplicate of bug #32980 and bug #33748.

In particular, see bug #33748 for workarounds.  The current workaround to increase the differences in the data above the noise floor of the single variables.  The easiest way it to subtract the mean from the data and then set the xlabels to your desired values by hand.

Closing report as a duplicate.

This issue has been reported as a bug against the Debian package octave (http://bugs.debian.org/783624).

Using the data in the file attached to this bug report (data.mat), the plot with gnuplot produces a correct result (see attached file gnuplot.pdf):

load data.mat
close all
graphics_toolkit ("gnuplot")
plot (data (:, 1), data (:, 2))

However, the result is clearly wrong with fltk (see atached file fltk.pdf):

load data.mat
close all
graphics_toolkit ("fltk")
plot (data (:, 1), data (:, 2))

Also, the labels on the vertical axis appear at the wrong places.

This is due to a bad conditioning of the data and the problem disappears when the data on the horizontal axis is translated:

load data.mat
close all
graphics_toolkit ("fltk")
plot (data (:, 1) - data (1, 1), data (:, 2))

This seems to be a bug in the fltk graphics backend.