Why is the Integration Active signal coming out of the back of my SC6000 camera not matching the time I set in the Camera Controller?

The Int. Active signal is actually fed to the FPA to start and stop Integration. However, the ROIC internally adds some extra clocks to the signal which adds additional time. This is the difference you are seeing. So, what you are setting in the GUI is what the FPA is doing but the Int Active Signal is shorter.  This is most noticable for very short integration times. 

The amount of delay between the end of the Int Active signal and the end of the integration period differs with the ROIC.

0209 (SC4000 InSb/QWIP) = 7.44us

0309 (SC6000 InSb/QWIP) = 7.44us

9809 (SC4000 InGaAs) = 4.4us

0002 (SC6000 InGaAs) = 4.4us

If you were trying to sync to the end of integration you would need to delay of this amount of time.