As for the A, B vs the S and C, nothing to worry about.
Seeing 0's on your transponders also is normally not a problem, unless it's on all of them.
Whats happening is that they are only using certian transponders and your area is not going to get all of them, maybe only a few, depending where your located and the DMA's spot beam.
You mentioned "Other" rec's, are they HD as well or SD, if SD , you probably would not see the same problems, if it IS HD and one does not do it while one does, then you need to check connections and cable on the bad run, possibly a barrel or a connector, maybe a BBC , lots of options till you start to break it down.
You could move your HD rec (bad one) to the other location, see if your problem still exists or not.
Thats a start.
Also, the locals you mentioned, are they coming to you thru D*, or with an OTA antenna ?
Jimbo