Using the Indian Ride Command Navigation System is awesome, but it still has an issue. After talking with the Ride Command programmers, they might hopefully fix it in the next firmware update.
I just had the same problem yesterday, I built a nice route on the ride command on my computer. Transfered it to the bike the ride command changed it. I ended up having to use google maps on my phone because the ride command was trying to make me do constant u turns. The first time I used the route building on ride command app it worked great. Not so much the second time. It makes me wonder if they even tested out before releasing it.