I apologize in advance as this will be somewhat long winded, but I want to try to provide as much information as possible to hopefully find an answer...

We have a Pixhawk with 3DR uBlox setup as a rover. Initially we tested the system on an RC truck, just to make sure we could get everything working the way we wanted, before we moved to our long term goal, which was setting it up in a boat. The truck worked near flawlessly, so we moved everything to our boat, and now we're starting to see major issues.

Our first trip to the lake was last Thursday, and pretty much nothing working properly. We couldn't even get simple functions such as reverse to work properly. So, instead of wasting time, we decided to come back to the shop and just redo the whole setup with everything in the boat as it's intended to be. After that, everything seemed to work properly. Switches, control surfaces, GPS, arming, etc. There didn't seem to be any issues. While that information may not be important, I figured I'd add it just in case doing a re-setup would be a suggestion.

Fast forward to our second day out at the lake. On our first attempt at putting the boat in the water, it seemed like the boat had almost no idea where it was at, although MP showed everything as correct (location, heading, etc). When switched into Auto for it's mission, it would go completely in the wrong direction. So, while on site, we decided to redo calibration, compass, etc just in case it was something going haywire from being so far away from our shop. After that, we put the boat back in the water, restarted the system, and things seemed to get even worse. And really, this is where it gets tricky/confusing to me...

If we pull the boat out of the water and start the system up, everything seems to work perfectly. The system initializes, we get GPS lock, arm, etc...all within maybe 15-20 seconds. Everything looks good in mission planner as far as direction, heading and all that. 

If we put the boat IN the water and start the system up, everything acts funky. The Pixhawk boots into the "police lights" and takes nearly a minute just to start seeing satellites. And once it actually gets GPS lock, it doesn't take but a few minutes for it to seemingly lose GPS. It's strange though, because the green light on the Pixhawk stays lit, yet mission planner says it has no GPS signal.

Regardless of which steps we take, the boat will only do 1 of 2 things. It will either head the complete opposite direction of the waypoint, or it will simply go in circles and nothing else. Even if we go through the entire setup on land and make sure it's GPS locked, then set the boat in water, we get the same scenario. It's like something is interfering once it gets set in the water, but I can't imagine what it would be.

We're doing all the testing at a private lake community in town, and the height difference from land to water isn't more than maybe 6" so I can't see that being a factor. These lakes are also extremely open in just about every direction, and we even took it to another lake just to be safe, but had the same results.

What makes it even more strange is that if we try to do a "Learned" mission manually via the transmitter, it still doesn't respond correctly. I can input the waypoints via the transmitter, they show properly in MP and everything, but once you set the boat in Auto, it acts like it's lost again. It does the same thing of either circling or heading in the wrong direction.

My only other thought is to get the system outside of the boat on a raised platform or something similar. However, I'm not confident that will do much because we get solid lock on land almost instantaneously, and we've even ran the boat with the top cover/lid open, so the whole thing was completely open to the elements with no change. Not to mention, I've watched videos of boats working without a hitch.

At this point, I'm kind of lost on where to go. We spent a total of about 4 hours at the lake, rebooting, redoing missions, etc...and everything led to the same results. I'm positive that there can't be anything wrong with our Pixhawk system as it worked beautifully on a truck. I also know that the boat itself works, as we can manually move it around the lake perfectly. 

So, now kind of I'm grasping at straws and open to any suggestions anyone might have. Even if that means trying out a completely different controller. A huge thanks in advance to anyone who might be able to help!