I am leaning towards the software. Sometimes, when you run consists of mixed PS2 and PS3 engines, something can happen and one gets scrambled. I thought it may have been fixed as it stopped happening here. I did change my habits and won't run a PS2 engine without first charging the battery. Some engines sit here for months without being used. So I had to rule out what might cause the issue.
I had a brand new PS3 engine get scrambled and I had to do a factory reset to clear it. I blamed it on the software. I then had another BN scrambled engine right out of the box and again was cured with a factory reset. Both those happened about a year ago and I've been fine since. So maybe it was engines made around the last year or two? There were a rash of them out of the box locked in direction or neutral I thought I had read about here from others last year.
Because it stopped happening I first blamed it on the older DCS release by nature, without pinning it down. The brand new engine that was locked made me think it was a software in the engine problem.