This occurs if the Simulator is open when you modify your Vector File and then re-simulate the design without re-loading the Vector File.
Once you load the Vector File in the MAX PLUS II Simulator and run the simulation for the first time, the MAX PLUS II software generates a Simulator Channel File (.scf) equivalent of the Vector File. The MAX PLUS II software uses this SCF when you resimulate. Therefore, if you modify your Vector File, you must re-load this file into the Simulator to use it to simulate your design. (Inputs/Outputs dialog box, File menu) Otherwise, the MAX PLUS II software continues to use the SCF created using the old VEC file to simulate your design.