I'm having a problem using the ATOM controller with Studio One multi-instruments and it really seems like a bug to me.
Try the following:
1) Drag an Impact XT preset from the browser, for example Artful Garage preset. This preset has a kick on the note C1
2) Select Bank 1 on ATOM (Bank key plus pad 1)
3) Play Pad 1 on ATOM (which plays a C1 MIDI note) - The kit plays a kick as expected
Now try this:
1) Create a multi-instrument (Browser->Instruments Tab->Multi Instruments->New Multi Instrument)
2) Drag the same Impact XT Artful Garage preset to the newly created Multi Instrument.
3) Select Bank 1 on ATOM (Bank key plus pad 1)
4) Play Pad 1 on ATOM. It should trigger a C1 and play the kick sound, but ATOM is now sending a C0 (you can clearly see this by looking at the keyboard at the bottom of the multi instrument window) so no sound is played. In order to get Pad 1 to send a C1 I have to set the ATOM to Bank 2 which seems like a bug to me...
In short, on my system, if I play Impact XT kits on a multi instrument, ATOM sends the notes an octave below what's expected.
Could anyone test this on your system to check if you have the same behaviour?