I imagine part of the problem comes with having your channel name come from your EPG or Services, and that leads to the service mapper putting them into different channels even though they are the same.
Personally I don't have this problem as all of my Channels are manually created, and the EPG Grabber settings are set to not update the channel name or number, only the icon. I believe the only way to consistently ensure your services map to the same channel regardless of network/adapter is to manually manage the mapping between services and channels. While it may be a hassle to initially setup, it may save time down the road.