Hi Peter,
Looks a bit odd in those images alright, I run a SBS system and although not imaging from both at the same time I can swap my camera from the refractor to the SCT and continue on without issue.
I have an Orion ST80 and SX Superstar for guiding and it's piggy backed onto the ED80 all running on an NEQ6 Pro.
So yes a couple of pictures of your setup may shed some light.
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