The code I posted earlier (p. 3), which only increments a variable in the ISR (serial is done in the work loop), demonstrates the same problem. I also wrote an even simpler version which sends a pulse on an output pin when the clock ISR is called. I compared the output signal with the clock signal using a DSO (which may not be entirely reliable for this application) and found that the ISR was not being triggered for most of the clock pulses. I can post this code if you are interested.
I would be interested, yes.
Again, the code you posted earlier is also doing a Serial.write on every HSYNC, and I can't help but think that is eating up a lot of cycles and again would suggest to maybe try storing those values in an array or something instead, and then Serial.write them out once you've collected a certain amount to see if that has any effect on the count?