Might sound obvious but do you have the i/p to the 4046 decoupled with a cap, there is internal biasing in the chip so that it can handle sine wave i/p's.
If you have decoupled the i/p maybe theres an issue with the i/p circuit on the chip, you could use an op amp maybe a lm358 to square up the waveform before it goes to the pll.
That is one heck of a difference in noise, one thing I've found with this ic is that there are some big differences between manufacturer, maybe another manufacturer would have better spec.