http://www.e-univercity.com/SynthGearDocs/
Not sure, but maybe this is what you need:
Take a look at E-MU Docs > Command Station > Command Station 2.0 Addendum - page 21 of 22.
Is your gear set up to transmit riffs? My thinking is as follows:
BTS sequences are special 16-track riffs.
The sequencer and the sound module are best thought of as independent (but connected) systems.
If the sequencer is going to trigger a bts riff, there has to be communication between the two systems.
Also look at the Addendum for OS 1.31.
Do you have the trigger note on the correct channel (i.e., the channel designated at the Beats Mode TrigCh?
If the bts are triggered from the basic channel, but the C1 in the sequencer is not coming from the Basic channel, that might be part of the problem.
Finally, look at the flow charts (aka block diagrams) at the back of the OS 1.31 Addendum (esp. the one on page 26--triggers and programmable knobs). I am not sure this is affecting what you are trying to do, but it couldn't hurt to make sure your settings are such that the data from the sequencer is going to the sound module in the way you want. This may not be relevant, though; I usually refer to it when making sure midi data is going into the sequencer.
Hope this helps.
Steve