I have multiple command stations, each with the RC-l01, and at least seven kerbals, and when they are the active vessel, they (most of the time) show themselves to be command stations, with the red dot. However, whenever they are not the active vessel, they register as ordinary vessels, and do not transmit.
In step form:

1. Fly the base or station that should function as a command station.
2. Note the red dot, and yellow lines extending to the tageted probes.
3. Switch to probes.
4. Note the lack of connection, no red dot on command station, and brownish lines connecting the two.

Mods:
Kerbal Attachment System
NEAR 1.3.1
Near Future Solar
Scansat 8.1
Dmagic Orbital Science .91
RLA stockalike
Procedural Fairings
Engineer 0.6.2.12
Planetshine
Remotetech (obviously) 1.6.2

Persistent save file:
file:///C:/Program%20Files%20(x86)/Steam/SteamApps/common/Kerbal%20Space%20Program/saves/Part%201/persistent.sfs