If at run time you place a frame on top of another no issues will arise, as I told you before. I have done that with UiEditor itself, when you see an Open dialog and also the Z-Ordering dialog. These frames are placed offscreen during execution and moved to 0, 0 when invoked via File->Open or Edit->Z-ordering.
Before I make any changes to that issue, make sure not to drag a frame into another. It shouldn't happen but it is happening, so it'll take some research to squash that bug.
However, if, at design time, you create your two overlapping frames in a non-overlapping fashion while you design them, then change their coordinates without using the mouse (by entering values in the editor in their Top/Left properties) you should be able to bypass the bug for now.
Another thing: You could manually fix the buggy .frm file that InForm output by removing the last parameter in the __UI_NewControl line when your frame was created and making it = 0. The last parameter is exactly an indication of the parent control.