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.
Takahashi FSQ 106EDX4
Sesto Sento 2 focuser
Paramount ME via TSX on RPi4
ZWO ASI6200 MM Pro
Chroma 3nm NB filters
Chroma LRGB filters
ZWO EFW filter wheel
Raspberry Pi 4 StellarMate OS at telescope
KStars/Ekos on linux desktop
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.