There are actually a couple ways that would make your BER 0. For example, the Duobinary design I sent earlier does not have a significant source of noise. To get a more realistic BER try adding a transmission link, like an Optical Fiber or a source of noise, like a White Light Source.
You also have to be careful with which component you are using, which could be the BER Analyzer and Eye Diagram Analyzer or the BER Test Set. The first two calculate the BER by directly analyzing the eye diagram. The test set actually compares the generated bit sequence and the bit sequence recovered at the output of the system. For all of these components the bit sequence length plays an important role on the accuracy of the calculation/measurement, especially for the test set since it is possible for bit sequence lengths of less than 1000 to almost never have a bit error.
Are you interested in plotting the BER vs Eye height and how it relies on the decision instant? Or do you want to plot the BER vs Eye height for systems with different noise levels or laser powers?