I was excited to see that Tower 3D supports "land and hold short operations" (LAHSO). However, it still generates a penalty.
Example: I had a CRJ cleared to land on PHL RWY 17 and instructed to hold short of 27R. The pilot read back that instruction. However, when I cleared another airplane for takeoff on 27R while the CRJ was still on the runway, I got a penalty.
The whole point of LAHSO is so you can do just that - it certainly should not be giving a penalty! The program should not be "looking" further down the runway than the hold short point when determining runway conflicts.
This is probably the same bug as discussed earlier with the penalty at JFK that should never have happened. Again, when you have an airplane making an intersection takeoff, the program should not be concerned with anything going on behind that intersection.
I realize this would involve some programming - you would have to logically break each runway into chunks, defined by intersecting runways and taxiways, and then determine for each landing/takeoff which chunks should be combined to determine the actual portion of the runway being used to detect conflicts.
I hope this can be fixed ASAP!