Doh! My PLLs lose lock. Crosstalk?

I agree that you need to check your PLLs supplies. Although you did say that you had removed the PLL and were using a high frequency osc. It might be your crystal supply as they are common to both.

One other thing I have seen in the past (cyclone II) is that you can get problems with SSN if you use a lot of the pins in the device and max out their current drive on LVTTL. You can reduce the I/O switching current down to min current, that seemed to help. The SSN causes caused wierd random failures.