I recently intalled a viper 5900 on my 94 civic si and the hood pin is not working anymore. I checked the brain to see if it had disconnected but it was still attached. I also checked the hood pin itself & everything is good. I also noticed my alarm led is not blinking normally & when I arm it my pager shows the hood being open.

 

This means even when your hood is closed the "brain" is seeing ground on hte pin wire (in a typical set up). Did the pin get re-adjusted perhaps where its too low for the closed hood to push it down? Also check for corrosion/wire breaks where the wire could be grounded.