Starting in 8.2i sp2, Architecture Wizard ties the REL port of the PLL_ADV primitive High, if it is unused. In this version (and previous versions), of the design tools, the REL pin must be tied High for the PLL to lock properly.
In 8.2i sp3 (and later versions of the design tools), the REL pin of the PLL_ADV must be left unconnected, or tied Low when REL is unused. Architecture Wizard still ties REL High, causing the PLL not to lock on the board.
This issue has been fixed in 9.1i sp3 of the Architecture Wizard. In 9.1i sp3 (and later design tools), Architecture Wizard will correctly tie the unused REL pin to GND.