Your first tuner seemed to be stuck in something, possibly EGP over-the-air scanning. The second tuner should be available.
Go to TV Options and click Manage Devices (or right-click "Manage Devices" on the "Television" tree). Select a device and click Configure. Make sure it's tuner type is set to DVB-S.
Next run "Load Program Guide...", also accessible on TV Options or Television tree, and check if you have any EPG loading method configured to run every day. Uncheck "Automatically load the program guide every day in the background", and uncheck "Run selected profiles now" before you click OK. Restart MC and try TV Setup again.
Also, make sure you are running the latest build of MC.