I was facing this issue from many versions of Indesign and don't know why its not been resolved yet.
I have a box or circle in which i have elements which are masked inside that circle or box. So when I try to resize it through transform Panel (not by transform tool), it doesn't resize its masked objects. I have tried different key combinations, also tried "transformations are totals" and other options it has, but nothing worked.
I really need this because to resize many such objects in a particular size, the transform panel is the faster way to achieve it with perfection.
Looking forward for a quick solution.
Here's an alternate method that should work: Use the scaling fields (width and height) in the control panel instead. The scaling fields scale both the frame and the content together.
By default these two fields presume the values are entered as percent, but you can also enter absolute dimensions if you include the units of measure (you can do this to enter numbers in different units in any number field in ID).
The scaling fields with units worked fine. Though ideally I believe it should work on the W and H fields too but no problem. For me its working. Till Adobe come up with a faster and logical solution will use this.
Thanks again Peter.