NIOS system generate, compiling and run trouble.

Any time you regenerate a system in Platform Designer, a new .qip is created. I presume you are using Standard, so make sure the correct .qip file has been added to your Quartus project.

Another option is to remove the .qip from the project and add the .qsys to it instead. That way, every time you compile your Quartus project, the system will get regenerated and you don't have to worry about pointing to the correct .qip.