there could be any number of possible reasons. can you provide more detail of the scripts you are trying to run?
1. number of groups you are running?
2. did the both tests run during same time of the day?
.
.
n. more along these lines?
is there a chance you could have run out of data you are using to run the scripts? meaning you only have sufficient data to run for 2hrs?
also do you have a contentcheck rule in place to capture any server error message being returned? what was your error count?
please provide more detail. thanks