Compilation process is funny in Quartus II

Are you running the Assembler from the Task Manager on the left? I'm not a fan of that flow because it tries to be smart. (I'm guessing there's something besides just "resting" that makes it think it has to re-do everything, but I'm also guessing that it's making the wrong choice). If you go to Processing -> Start menu, all the individual commands can be run, and there are no "smarts" behind it. If you tell it to run the assembler, it runs the assembler. If you tell it to run EDA Tools, it runs those. Now, if you had never fit the design, the Assembler will give an error and say the fitter must be run, and it won't do it for you, but most likely in your case it will do just what you want.