Is the program capable of doing frames (with shear and bending members) as well as true trusses (axial loads only, no shears or moments)?
If so, you can get a singular matrix if you put too many pins in your member ends. In a typical frame analysis program, every node must be rigidly attached to at least one member, even if all members are notionally pin-ended at both ends. Otherwise, the rotation at the node is undefined, and the matrix solution will fail.
Check the documentation for your program for more information.