We are using a Multi Box with 6 levels of hierarchy. We have a dimension that contains only one selection within that dimension. Qlikview automatically displays this selection, making it seem as if it is selected (when it is not).
Example:
A
B
C
A has dimensions 1 and 2, within 1, B has dimension III and IV, and within III C contains only dimension v.
Surely in this case 1 and III are highlighted in green, whereas v is not? It is the colour that denotes that a selection is made, the fact that a value is shown on denotes that only a single value for that field exists within the selection.
Conversely to what you are describing if multiple values are selected for a single field, their values are not shown in a multibox - rather just a green spot.
I think that once you explain the Green, White and Gray to your users it may be a non-issue anyway. If not you may want to look at providing an alternative way of seeing what is selected, for example a Current Selections box, or output from the function GetCurrentSelections().