Due to a problem in the Quartus® II software version 11.1 SP2 and earlier, the Invert Signal menu option is disabled in the SignalTap™ II Logic Analyzer.
To work around this problem, close the GUI and edit the SignalTap II Logic Analyzer (.stp) file in a text editor. Find the line for the signal you want to invert such as:
<net is_signal_inverted="no" name="<signal name>">
Change the "no" to "yes" and save the file. Re-open the SignalTap II Logic Analyzer GUI. The signal is inverted.
This problem is fixed beginning with the Quartus II software version 12.0.