There have been some cases reported where a laptop's TTL output levels have been too low (3.3v) to work with external hardware. Most of the time, external hardware is expecting to see a 5.0v signal as a logic '1'.' Some laptops just don't send a strong enough signal to register.
One of our users did post a sample MediaLab experiment which successfully interfaces with an eye-tracking system:
http://www.empirisoft.com/support/showthread.php?t=152
Can you post a link to the Biopac system you're using?
Does anyone in your lab have access to an oscilloscope - or at the very least, a multimeter - that we could use for diagnosing the problem?
John