Well, 'issue' is not the correct way to describe it.
The 'Stereo' and 'Multichannel' output presets are just that. If you have any SD3 Preset with a setup with faders going to Buses, then apply the 'Multichannel' output preset, which will direct the individual mic faders to different outputs per instrument, then it will naturally break the mixer part of the preset.
Just selecting the 'Stereo' output preset again will simply direct all faders to the 1 st Stereo output and the faders previously routed to Buses for EQ and Compression will not be routed to them.
Remember, those are just output presets, not enabling or disabling the actual plug-in outputs.
If you wish to have FX, EQ, Comp etc intact but on separate outputs, please learn how to direct the Buses to separate outputs.
BTW, these outputs can have FX, Comp, EQ on them as well before going to the DAW mixer.
BR,
John