Just want to let people know that may have this same issue. I think I found a work around. At LAX when I start I only activate 24R and 25L. I can still have them take off from 24L and 25R and I don't seem to have the Runway Alert issue. Maybe that's the way it's suppose to be set but I always thought you had to have all the runways you were using active. It also makes it so I don't have to keep changing landing planes to the other runway, they always come in on the runway I want them to.
I also found how to re-set the score because I was something like -5000. While I was in the reg I noticed that your reg entry for the control hours is set to a 32 bit DWORD and it's saying the value in it's invalid, looks like a binary entry, probably why the control time is always 00:00.