I think Lynn was correct in suspecting a memory issue.
I will venture a guess that after 12 hours you getting the trigger you are looking for.
After the trigger the history is read and formatted for file.
Now it is time to math.
After 12 hours of 50,000 samples/sec on 16 channels you have alot of data.
I wipped a quick test VI to help figure out how much memory is being used.
You are collecting 800,000 samples/second.
Formatted as text, the string length is 4G (that is for one second).
For 12 hours you need 2.1 tera bytes of memory to buffer the string!
So....
I would suggest that you truncate the data to a couple of seconds prior to the trigger event and save the data as binary.
Do post processing to convert it to text
latter.
I hope this helps,
Ben
Demo attached