The problem may lie in the fact that the search algorithms for the various Alice Drag 'n Drop features don't always work the same.
An example of proper functionality would be the "(what) as a string" function. It includes the groups as part of it's search of the Object Tree, while commands like if/else may not.
An easy fix for this is to do all of the coding before you compress a myriad of objects into a new group. If, later, you need to add code for a specific object, remove it from the group, make the changes, and put it back.
Doing so will not break the code, nor lose the linkages.