Your netlist at 
http://www.dhandanought.org/tcpip/audio/EXP/geda-probs/test-schem.net
does have all the connections made in the schematic....  The schematic
shows no connection to
B or C on the transistors.  siggnd has  Q2-E which is all there is for Q2.
Simple as that.
Q2 pin E is connected to net siggnd.

Great. Thanks for identifying this.

What I really need to know is how did this happen? When using gschem, I
tried moving each transistor to check whether the nets were connected to
the pins or not, and they moved with the symbol, showing connection.
After that, why did the connections not show up in the netlist?

Tarun


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