John,
What would make certain areas different than others?
Polarity makes a huge difference with DCS. Engines look for commands on the center rail and send commands back on the outside rail. It is absolutely essential that the DCSRC Receiver's red post is connected to a center rail and the black post to an outside rail.
Further, the DCS signal cannot get to any track block where the center rail is not connected to the same transformer terminal as is the track to which the DCSRC receiver is also connected. That's why a DCSRC will work with one transformer handle only.
I suspect that somewhere in the wiring around your DPDT switch you've inadvertently swapped the wires from the transformer on some of the blocks, so that the wire from the DCSRC's red terminal is connected to that track block's outside rail, rather than its center rail. On those blocks where the wires are swapped, any PS2 or PS3 engine is going to think DCS is not present on the layout and will come up in conventional mode.