"Our other problem is that we took our timer out of the box and ports 2 & 4 do not reconize inpulses. Any ideas?"
1. The device is polarity sensitive - check that the impulse cables are green on green, black on black.
2. Check the "Input Status", for each input it should be set to transmit/arrow up.
See 5.2.4 in the user manual: http://www.tagheuer-timing.com...l/en-US/CP540_EN.pdf
If you are still having problems it would be nice to know the version of firmware.