Eventide Staff
Piet,
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:
http://www.eventide.com/AudioDivision/Support/Stompboxes/PitchFactor.aspx
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 support@eventide.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.
-Russ