More poking around - I really don't want to get a payday-advance to pay rent this month.
In version 13.1 the ALTPLL wizard never comes up. The 'Add Module' screen runs for a bit, changes to 'Edit Module', then goes right back to Qsys.
In version 13.0 the ALTPLL wizard will finish. Goodness knows if the output is usable; that's the area in my design that seems to be causing all the problems.
In 13.1 'Altera PLL' will finish. That IP is greyed out in current versions which makes me nervous about using it.
Note to Altera: The ALTPLL wizard seems to have gotten broken starting with version 13.1 - my guess would be that Linux updates since then have rendered it useless.
Question: Does anyone have a work-around? Any chance that this defect will be addressed?