If you migrate older designs into Quartus you may get some internal errors and the program may crash. I had dug into this some time ago to find the root cause of the crash and spoke with Altera who confirmed the problem. I just installed the most current version of Quartus and the problem is still there.
So, if you run into this, look in the .QSF file and see if the following line is included:
set_global_assignment -name TDO_DUMP_FILE AUTO
If there is, remove it and try to build. I am not sure what versions of the Altera tools added this command, but starting with Quartus 5, it will crash the program.
Hope this saves someone some time ......