So if you are counting time between photons, you are essentially using the photon signal edge as a trigger and the clock as the source, and taking continious retriggerable counting. This will only overrun if the photons come in at a faster rate than you can read from a buffer, 100kHz is not fast enough to cause a problem, but make sure of this:
1. Make the buffer big enough to hold at least 1 second of data - that is at least 100,000 samples.
2. Read the buffer faster that 1 second and read all points. I would suggest to use a producer consumer loop where the data is read fast 10Hz and ququed up to an asynchronous loop for processing and display/file IO. (see producer consumer template)
3. MAKE SURE YOU ARE USING THE DMA CHANNELS*** the 6602 has only 3 so use 2 for your counters.
4. Disable the CI.DupCountPrevention, this is true by default and will filter out events with zero (probably not going to happen in your case since the 80MHz clock is fast enough to have many counts between photons.)
There is no reason that you will ever get a buffer overrun if your photons are not comming in faster than 100kHz and the trigger is clean.
Paul