interrupt starts at different times depending on upload time of program

Can you explain exactly what the timed sequence you're trying to achieve is, and what timing resolution you're trying to achieve for each part? I mean, I guess you're trying to trigger the camera while the LED is on, but I have no idea how long the LED will be on for, how much latency there is in the camera at the start of a shot or how long it needs to take a shot. Since the overall process is only repeating at 230 Hz this seems like the sort of problem that could probably be solved without interrupts but if you need really small latency you might be forced to use them.