Cyclone 4 ALTPLL wrong freq output

There might be few main reasons for PLL to not work properly:

1. Excessive jitter on reference clock (check PLL input jitter specification in datasheet)

Personaly never had issues with jitter.

2. Power supply is not connected on VCCA VCCD_PLL GNDA pins.

I think that there ar very litle chance that you have two boards with same soldering issue. I would rather go for schematic error.

3. Power supply noise

Had this issue once. Check power suply noise requirements

4. Wrong PLL configuration.