I explained this a lot to the different project participants at the beginning of the project. You can't know in advance if the calculation will converge and how long it will take. The consequence is unpredictable calculation times and invalid tasks when the chemistry doesn't work. This is how we explore the frontier between combinatorial chemistry and what is theoretically possible and stable. Scientifically, the invalid tasks are very important because they will allow us to train models (Artificial Intelligence) which will allow us in the future to predict the validity or not of the molecules studied with a good precision we hope. At the moment, we are already using these data and the results are encouraging.

There is absolutely nothing wrong with the native app other than the assigning of core/thread affinity. Take that out of the executable so machines can use all threads and you have a winner. Like Michael, I've been running it with a affinity script and it works quite well.

Curious behaviour... At the moment, I have no idea.

Energy saving configuration ? Boinc client that decides to switch tasks ?