The most common reasons for this are:
If the values are constant, but non-zero, then you are most likely capturing scattered photons from the atmosphere. Check if you are simulating a daytime collect where the solar scattered path radiance might mask your active signal.
The signal gate is starts after the photons arrive from the scene or it is stops before the the photons arrive from the scene.
The active flux is too small because the pulse power is too low, the diveragence angle is too large, the throughput is too low, etc.