Shift register on sync RS flip-flop
I believe your problem comes from the clock signal you're using. Its positive pulses last for about 100 ps or less, and the flip-flops probably don't have enough time to react to them, which leads to sporadic errors.

Find the maximum switching frequency in the spec of your flip-flops. It is usually given for a clock signal with 50% duty cycle, so you can take half of the period and assume that positive pulses of your custom clock signal cannot be shorter than this value.