need help with Slic3r creating supports overlapping object  

need help with Slic3r creating supports overlapping object

Hi all,
I could not find this by searching but maybe it has been discussed.

I am using the Mk2 with multimaterial and normal prints (1 color, or prints without supports) work great.

I have an STL file that I created with 2 separate objects in 1 file. The object needs supports. I want to print using 2 colors. I load it into 1.41.2 Slic3r, and if I just slice the single STL all goes well and it will print fine.

the problem occurs if I split the object into 2 objects. this also looks fine, and the objects are properly separated.

the problem becomes the supports. Slic3r seems to not understand the presence of both objects when it generates supports.
The supports for the first object actually overlap the second object. the other way around is fine - supports needed for the second object do not overlap the first object. It sems as if the second object is not considered when the supports for the first are generated. This can clearly be seen when previewing the sliced output using single layer view. in the layer it shows supports drawn on top of object 2. it prints this way as well.

this problem makes the supports impossible to remove since they actually lead right into and through the other objects.

how can this be fixed/ or is there a better workflow for printing a combined object using 2 colors with mmu? the relative position of the 2 objects is critical and they cannot be separated or combined once printed.