I think the problem is, partially at least, that if you get the hardware to force the output pin low, it is put high immediately, not when the timer starts.
Would it help if I made the exposure occur during the HIGH period? The reason I designed the TTL circuitry to shutter on LOW signals is that is how the timer seemed to work when set up with the Timer1.cpp sample code. It went LOW for the first phase of the PWM and HIGH on the second phase. When I turned off the timer in the interrupt, it just stayed HIGH. I see in your code that you specifically set the pin high before you disable the pin. I understand that it might be possible to invert the PWM outputs. I can mod my board and bypass the inverter, and change the board design when I order more.
Let me know if this give you more options.
Wine with breakfast? I'd go with a Mimosa.