I would have said you didn't have the write file, but I have a Q8.0 Cyclone III design in front of me that has a PLL and compiles. I opened the altpll.tdf file, searched on the "include", and see the same lines you're seeing, i.e. no mention of Cyclone III. But interestingly, mine are at line 448, so there is something different between our two files, even though we should be using the same version of Quartus. Can you check:
a) The header at the top has a build. Mine says:
-- 8.0 Build 215 05/29/2008
Can you check yours?
b) Check what directory your file is in? Is it the Q8.0 install? (Are you installing Quartus versions into the same directory?)
Finally, perhaps try re-opening it in Quartus, making sure the targeted family is SIII or SIV, and re-generate.