You should download the latest 3.5 beta release for Pitchfactor. From what I'm understanding, it should fix most of your problems. You can get the Eventide Update Utility here:
Once you have it installed you'll need to set up a username and password, and then you'll be able to connect and download the update to your pedal. Contact email@example.com if you have any trouble updating.
As for the parallel loop out of phase problem, well, that's too be expected. The PF is a digital device and it will inherently add some small amount of delay. For parallel loops we always recommend KILLDRY. I assure you, it's nothing out the ordinary.