My guess is that the code to create the second figure uses
grid on
without being careful about what the current axes is.
A lot of code relies upon a sequence such as
figure
plot(....)
grid on
which rely upon the "active figure" and the "active axes" be what the programmer expects. Unfortunately there are circumstances under which the active instance might have changed unexpectedly. It is safer to write code that always explicitly gives the handles that are being acted against:
f = figure;
ax = axes('Parent', f);
plot(ax, ....);
grid(ax,'on')
