PLL Megawizard broken in Quartus 13.1?

Usually, Quartus autmatically adapts megafunctions during compilation for the desired target platform, whereever this is possible. This applies e.g. for RAMS, etc. Unfortunately, this does not work with PLLs in this constellation. I had the problem that I wanted to convert an existing design running on Cyclone III and Cyclone IV to a Cyclone V platform. When I tried to compile my design on the Cyclone V for the first time, I received errors indicating that the "old" PLL could not be instantiated. The reason is, that the PLL in the Cyclone V has an entirely different architecture compared to Cyclone III and IV and it cannot be converted automatically. To support the Cyclone V PLL, Altera has even introduced an entirely new wizard. I received similar problems for other megawizard functions, e.g. the ALTMEMPHY and the remote update unit that are also not compatible with Cyclone V any more. I could suggest the following according to your situation: Either you try to instantiate the PLL directly but this leaves the burden of setting all the complicated PLL parameters correctly to you and this is much effort and requires deep knowledge about the internals of the PLL. Or you create the PLL on your laptop where the wizard is running fine. Afterwards you transfer the megawizard generated files to your "main" PC and add them to your project there. This should work since compiling the PLL is not an issue. Finally you may consider switching back to Quartus 13.0sp1 since the bug is not present there.