Something besides hold is causing the issue; hold by itself only toggles the state of whether subsequent "stuff" is added to or replaces earlier "stuff" on the axes.
Pare an example down to the minimum it takes w/ a set of random data to illustrate the problem...something like
figure
plot(rand(10,1))
hold on
plot(sqrt([1:10])-0.5)
Then, add what it is from there that you're doing in your case to cause your symptoms and if that doesn't give you the answer of what not to do or how to fix the problem, post that series of commands.
