I personally don't use PHD2 so I can't respond to any questions about it. I just use the internal guide functions from KStars native.
AS for the capture, have you tried new cables?
Have you tried hooking the ASI1660MC up to a Windows desktop and seeing if it will perform a 1s capture using the ZWO software?
The EAF should not be having anything to do with the time it takes your system to capture a frame.
Honestly... when I have issues like this I just copy my capture data off to external media and then blow out a new image of whatever version I want to use. I have 1.7.7, 1.7.8, 1.7.9, 1.8.1 and 1.8.2 kept on my computer and a thumb drive in case I want to install one of the older ones. Which reminds me.. I probably need to go ahead and download 1.8.3 also to add to the group.