I had a question for ADF4157 and please see the attachment.
While I had write all registers and why the phase seems shift the 90 degree??
I'm assuming the phase jump happens after a write to R0. Every time you write R0, the ADF4157 will re-lock to the desired frequency. This re-locking process causes the phase shift you are seeing.
As an experiment, you could try disabled sigma-delta reset - set R3, DB14 to 1. This will disable the resetting of the sigma-delta modulator and may remove the phase jump.