I did not use swap. You are placing things in one place then swapping them over. Please try without it.
There is no sky atlantic on cable. Remember, you are using a HD lineup, so that chanenl is in the right place. You will need to edit/add that line to insert the SD one.
With regards to the duplicates, does the sentence quoted below not make sense? They are meant to be there. I suspect You have previoulsy been looking at the "region custom" output of ABM. This omitted the unavilable HD ones, so you only had the SD ones.
Please confirm that youhave removed the custom lcn file. I had issues and almost filed a bug report. Run it five times, cahnging other things before the penny dropped.You will still have channels further down the bouquet. If you want to omit them, have a look at the the xml. There is a section for deleting channels.
Also, while you are in test mode, please enable the service type icon.