How are you connecting the LCD/shiftregister? Via two or three wires? As stated, some (me included) had trouble getting the two-wire method to work with a HC family shiftregister. I am not sure why though. I guess the same applies to HCT. You can either try with a LS type shiftregister, or use the three-wire method (unless you are already doing that, in which case I do not know what the issue is).
Maybe if you posted the code related to the LCD it would help, as well as the schematic you use for the LCD.
Also, as TBAr explains, the analog inputs 0 to 5, can be used as digital I/O 14 to 19.
I am also using Ubuntu 9.10 and usually arduino-0017 btw, but I do not think that is the issue.
I have an old HD44780 compatible one-line LCD as well as a 2-line LCD named "JHD202C", which both works fine with the library.
As for using your 2nd line, you must first initialize the display correctly. The functions are explained in the usage page
ShiftRegLCD srlcd(Datapin, Clockpin, Enablepin or TWO_WIRE [, Lines [, Font]])
Or, if using three wires, and a 2-line display. Enable will be on pin 8:
ShiftRegLCD srlcd(12, 13, 8, 2);
srlcd.home(); // Set cursor position to zero
srlcd.setCursor(column, row); // Sets cursor position
Remember row begins at row 0 (zero), for the first line. Also column begins at column 0.
Hope this helps.