Reply to LED's not changing with toggle

I'm not exactly sure if this is a firmware issue, but I recently started having some problems with my VCI-100.

I upgraded the firmware with no issues and have been using it for a few weeks with absolutely no issues. However, last weekend Traktor crashed and everything froze. After a reboot Traktor was back to its default settings and after I loaded Ian's TSI, none of the lights works as they did before. None of the effects buttons light up when toggled, my effects bank selection LEDs on the left don't work, 'Copy to C/D' won't light up when toggled. You get the picture. Any ideas about what's going on?

Here's some info on my set up
VCI-100 firmware 1.3
Traktor Pro 1.1.1.001
Macbook Pro - OS 10.5.7