Sounds like you have just 1 capture card installed which provide you 2 Encoders. This is happening at my install with a WinTV Nexus-S DVB-S Capture Card.
You can choose in mythsetup how many recoders that capture card is providing and the default is 2.
But Encoder2 isnt a fully Encoder when Encoder 1 is in use,it can only provide the channels which come on the same transponder from DVB-S.
I have 2x capture cards installed,1 in the core and 1 in a md.But i cant get the 1 in the md to run.I have prober firmware installed from linuxtv and i can choose it in the setup as new card,i can choose the LNB and have a lock on a channel scan.But in mythweb statuspage the Encoder is always listed as currently not connected.
Howie