Hi DirkW,
Thanks for all your help. Sorry for not replying sooner to your previous post.
Unfortunately the timing is still inaccurate and sometimes it tends to report negative times still. 
Perhaps the LIN 8476 device is not accurate enough for this type of measurement with its timestamp?
Your previous mail mentioned accuracy to 1us with 1kHz DAQ, maybe you meant 1ms ?
As a solution I have used a scope to measure the time and I have connected it via GPIB and am now measuring it that way.
The disadvantage to this of course is that it is not flexible if an array of LEDs were to be measured as the scope lead would have to be moved each time, but it may have to do.
Thanks again.