I just reported this through an Adobe Bug Report form, but I'd also like to post it here publicly, so others can be aware of it.
The problem happens also with the "Copy" button when double-clicking the Move tool.
A work-around for using alt-drag and Duplicate to quickly generate several instances of elements, can be achieved by using the Transform Effect, which seems to produce the expected result correctly.
I can supply a fairly simple but already misbehaving example file, if necessary.
******BUG******
Concise problem statement:
Alt-drag to copy elements in a complex file with layers in layers, produces not the same result as a normal Copy & Paste.
Steps to reproduce bug:
1. Draw elements on top of each other and include some nested layers (so not just nested objects like groups, clipping masks, compounds, etc.)
2. Drag the whole bunch with Alt key. You can see all elements correctly moving in wireframe view.
Results:
The elements which were stacked in a nested layer get copied within that sub-layer, yielding a totally different result with regards to the stacking order.
Expected results:
A new stack of all layers and their elements (including the sub-layer) correctly on top of each other and the original elements.
