I can't see anything... those screenshots are zoomed very far out and the aliasing is terrible.
Please show the input waveform in comparison (both on screen simultaneously, trigger on input). Is the rising or falling propagation delay the problem? This should be evident at any frequency, and as you raise frequency you'll clearly see the propagation delays overlap and then the output disappears.
How much does it depend on distance (between emitter and detector), or drive current? Should it be tolerant of such variations? Can you tune it for a particular condition?
What about ambient light, should it be tolerant of variations? Or will it be in a black box, well shielded from that?
And what kind of signals are you looking to communicate here?
Tim