‘Invalidated By System’ messages appears when you restart the service and there’s a job in a ‘running’ or ‘pending’ state. The jobs that were running between the restarts need to be reset (because the thread that is executing the analysis is killed, so on restart, all you can do is mark all running jobs ‘failed’ with ‘Invalidated by system’.
The original problem you were having is strange: you say that you click ‘generate’ but the job just sits in pending status? It’s possible you have another error happening between starting the job and the job starting the execution. Do you have anything in your logs? You mentioned that it did run successfully once. Can you get a simple cohort to generate or revert to the version that was working?