I agree, something doesn't sound quite right.
As you said, if it is a 24v system, you got the thrust wrong. I have had 2 terrovas. One was a 55lb. thrust 12v system on a 16' aluminum deep v. It was weighted down with a 75hp motor, 30gallon bait tank, and 2 guys. We would use the motor heavily for catching bait in the morning, and then troll for stripers, sometimes 6-8 hours. The battery never went dead on me.
Next boat I got was a 20' dual console with the terrova that I now own, an 80lb thrust 24v system. Same deal, troll all day long, no issues. I run the motor on 1-4 most of the day, with some spurts on 10 here and there to get onto a breaking school when I have 12 lines with live bait out. That system has never let me down either. I have fished 2 days back to back and still not run into any issues.
All that being said, I have never run full blast for an hour straight. If I were trolling that fast (3 mph) I would certainly get a 4 stroke kicker motor.
According to the minnkota website, the 24v motors require a 60 amp breaker and 36v require a 60 amp breaker as well. I actually have a 50 amp breaker on mine and have never tripped it. That tells me that at full blast the 80lb motor uses just under 50 amps per hour at full force. Now take two 100 amp hour batteries. You have 200 amps reserve, but only want to use 100 amps (do not discharge Lead Acid DC batteries past 50% for longevity). You would get about 2 hours run time at full speed.
Verdict is in! If you want to troll at 2-3MPH for more than an hour or two, you need a gas motor!!!!