1 Correct answer
I just tried scaling in InDesign CS6 and had the same issue so this must be a long standing bug. As with InDesign CC, using the Control panel to scale works fine in CS6.
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Couple of things to check. In the Stroke panel, choose the alignment for the stroke. Sounds like you may want "inside".
Also, select the object with the stroke and in the Transform panel, uncheck "Adjust Stroke Weight when Scaling" before you resize the object if you don't want the stroke weight to change.
Hi Barbara, thanks for the response. For the first point, I definitely do not want the stroke inside. I want two identical shapes, one directly atop the other, with the bottom one having a stroke so the shape is outlined. If the bottom shape has an inside stroke, it wouldn't be seen at all. To the second point, the stroke is not adjusting with the scale. I start with a 4pt stroke, and after scaling, it's still a 4pt stroke. Which is exactly what I want. BUT the physical size of the two shapes are different!
Here you see the top layer - the red circle on layer 2 is selected. Info shows the size of the shape as 18p0 for height and width. The red circle layer has no stroke. You can't see the blue circle beneath the red, but you can see the stroke on the blue circle and it seems to outline the red..
In this one the bottom layer - the blue circle with the stroke is selected and the red circle is hidden. The size of the shape is exactly the same.
In this image all the layers are selected together.
Then I take the selection tool, hold shift, and scale the two images up. Notice immediately that the bottom blue circle is no longer hidden beneath the red one. Note the size of the top layer, which is 40p7.529.
Now we hide the top layer and look at the info panel for the bottom blue layer. Its size is different from the top red layer. It is 41p8.1!
My strokes are exactly the way I want them, and they're working as advertised. However, I can't for the life of me understand why InDesign is making two identical shapes two different sizes when they're scaled together. THAT'S my problem! Thanks again for the help! 
By default InDesign recognizes the stroke of an object when calculating its size and reporting it in the Transform Panel. If you want to have the sizes shown without including stroke weight then uncheck "Dimensions Include Stroke Weight" in the Transform Panel pull-down. See screen shot:
Hi Bill, thanks much for the response! I really appreciate you guys taking the time to help me out.
Since I didn't want the weight of the stroke to change or figure in on this, that transform panel was the first place I went. Here's how my transform options were set up for this...
Do you happen to know if there's another place in InDesign where this option may be active? Like maybe a preferences check box I don't know about or something like that? It has to be something like this because the objects only differ after scaling IF the bottom layer has a stroke.
In the General section of your InDesign preferences select "Adjust Scaling Percentage" rather than "Apply to Content" under Object Editing. See screen shot:
When you do this the Transform Panel will report only the dimensions of the shapes as if they were drawn with no strokes at all. The reality though is that if one of the objects does have a stroke applied that goes outside the original boundary then if you physically compare the two the one with a stroke will in actuality be larger.
Hi Barbara, haha I was thinking BUG, but I wanted to hold out hope I was just doing something stupid. I appreciate your help and effort. It's much appreciated.
Since I actually need to adjust the shapes visually, it looks like I'm going to have to switch to Illustrator to do this project (since it doesn't have this problem). Of course, I have a feeling I'm going to run into some other unseen problem, so don't be surprised it you see me in the Illustrator forum!
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