When I am using the tool, I get another result which looks plausible to me. Did you use the following input (which is the given structure):
vars a,c,d;
init 0,3;
labels 0:; 1:; 2:c,d; 3:; 4:; 5:c,d;
transitions 0->1; 0->3; 1->2; 1->3; 2->3; 3->3; 3->4; 4->3; 4->5; 5->3; 5->0;
and did you compute K1≈K1?