Talked to the mechanic at the dealer and he said there's 4 safety switches. Clutch, PTO, and Both HST pedals. Any one of them may be out of adjustment. So I have something to look into tomorrow when I go back out there.
As stated before the lynch pins probably worked themselves out due to the heavy brush I was working in. I like the bolt idea for attaching to the tractor, I see no need to ever remove the arms, so it's not like it would be an inconvenience or anything.
Thinking back to using the Bad Boy rotary cutter yesterday, it was having no issues at all and I was cutting through some saplings as big as 1.5 inches. Never bogged down the engine at all. Compared to the unit I rented that was 39HP this one actually did a better job. I'm not sure if that's just because the new cutter is sharp and new or because it's a 4ft vs a 5ft on the rental tractor.