Both the Digital Lynx SX and ATLAS acquisition systems utilize a 5V TTL digital I/O port.  To properly trigger a bit change on the hardware, the input voltage must transition from 0V to 5V.  Any voltage lower than the 5V could cause the bit to bounce or trigger more bit changes than intended.  Additionally, if the voltage is too low, the system will not see the change at all, resulting in no bit change being recorded.

The grounding of the port/bit is as important as the proper input voltage.  If the corresponding bit's ground is not tied to the output device ground, the bit is effectively floating, and this can cause the bit to have false triggers, or not record any triggers, even with the correct voltage applied.

If you are having any issues with the recording of TTL inputs, there is a simple test that can be done to ensure the hardware is functioning properly.  Be sure to have Cheetah or Pegasus acquiring during this test, otherwise no bit changes will be seen by the software.  The top right bit of both physical ports is a 5V power pin (see image below).  Shorting this 5V power pin to the bit below, or any other bit, will cause the system to trigger bit changes.  The changes will be random, as this is not a simple High to Low voltage change, but it effectively indicates if the system is able to properly observe TTL bit changes.

Additional information can be found in the SX users manual and Cheetah/Pegasus Reference guide.