In designs where the user reset is active low, an inverter is required to drive the active HIGH reset pin of the MMCM. In some cases, the inverter is incorrectly optimized out of the design so the MMCM is permanently reset and does not lock.
The workaround is to add "Save Net Flag" or "Keep" constraint on the reset signal (in HDL or in the UCF) and rerun implementation.
NET "*mmcm_reset" KEEP;
or
NET "*mmcm_reset" S;
This issue is also fixed in ISE 12.2 and later versions of software.