Here is a little more information on the BER Test Set:
In the BER test set we provide multiple binary sequence generation options: a PRBS generator, User Defined sequence generation, or external Sequence. The PRBS and User Defined sequence generators are exact copies of the PRBS and User Defined sequence components respectively. HOWEVER, the default values for the number leading and trailing zeros is not the same. The PRBS generator inside the BER test set takes its number of leading and trailing zeros from the layout parameters and has default values of 0. The PRBS component defines the leading and trailing zeros within its own component and has default values of “(Time window * 3 / 100 ) * Bit rate”. This can make a big difference. Try setting them the same for a better comparison.