There seems to be some configuration that will not allow Programs to run. I eventually reinstalled everything and it appears to be working now, the biggest change I made were the following:
Weather Adjustment Method:
Auto Rain Delay -> Zimmerman
Prior to this the Water Level % was 0, now it is 74% (have no clue what this actually means).
Also, I did not see the red line signifying the current time in my previous where as I do now. Could it have been a bad initial install?