Depending on the IO voltages of the signal recorded, and the IO thresholds in use of the logic analyzer, these thresholds may not be well matched. This usually results in an exaggeration of the duty cycle. For instance, if you are recording a 10-volt signal but the logic analyzer has a logic threshold specifically for 3.3-volt logic (1.65 volt threshold in the case of the Logic Pro devices), then the logic analyzer will most likely interpret the rising and falling edges as predominantly high, causing the recorded duty cycle to be higher than expected. Ideally, the logic analyzer would interpret the exact halfway point of the transition to be the point where the signal switches between high and low. However, in the case of a 10-volt logic signal, the threshold of the logic analyzer would need to be 5.0 volts, which simply isn't supported. It's okay to use a non-ideal threshold voltage to record a signal; it just won't produce ideal timing results. In most cases, that should not be a problem.