By "overlapping groups" I assume you are talking about groups that contains stacked islands.
I am not sure to understand well your problem. But in order the staking group system works well, all islands that are grouped and stacked in a same group must be stacked perfectly (all island must be located exactly at the same coordinates). If you respect this, spacing is working perfectly with stacked elements.
To create a staked group simply select one island of the same family and in the "Island Groups" panel click on "Stack". The islands will be stacked and a stacked group will be created.
I think the better solution would be that you send us the log file and the OBJ file. (you can use wetransfer and send to firstname.lastname@example.org)
This is still broken for me i still get overlaps on stacked shells seems to be a problem if i have edited them in an external program using fbx with unfold bridge in 3dsmax, makes the packing useless to our studio, any ideas why this is happening?