I ran into the same problem with the latest stable build (3.6.0 Stable) The guide scope appeared as primary scope but it does not suspend phd2 guiding.
While we are on the topic of suspended guiding, is there a simple way to delay the first image of a sequence after autofocus to allow the guider to stabilize - say 10 or 15 seconds? My first image is not usable after autofocus with suspended autoguiding.
I believe you can set the guiding deviation under a threshold which the sequence starts (i.e: if the guiding RMS above 1 arcsec then the sequence won't start). See it in the capture tab.