It is hard to say exactly what is causing your large measurements but your additional comments gives me a clue.
When you see this issue it is not in the VI you supplied but in another VI that has the graph.
I susppect you are running into the indeterminism of Windows. This prompts me to suggest you go to a hardware time acquisition. By using one counter's output to gate the conter and your TTL pulse to incremet it, you will be able to avoid the peculiarities of Windows.
What I am genarally guessing is happening now is;
The is no garentee when the start of the counter and the start of your wait. The wait will timeout when the next even multiple of 1 second occurs in the millisecond wait timer. If the starting of the timer is delayed because Windows wants
to go refresh some window that you may or may not want to look at, then the conter does not start when you expect or the wait timer.
Going to a hardware timed scheme, you do not have to worry about windows.
Ben