I've got a similar issue with containers in one of my documents and haven't discovered why it is just this one document affected. I am able to open the document with the containers sized correctly when minimized, but if I close it (without saving) and re-open, the containers are shrunk to 17x17. My developers working on the same document don't get the problem when they do the same so seems to be something with my installation.
I have set up a macro to reset the containers which isn't ideal but at least lets me work in the document. One note is that the containers must all be minimized for the macro to resize correctly. Hope this gives you some ideas ...
for each x in a
set ct = activedocument.getsheetobject(obj)
set ctprop = ct.GetProperties
ctprop.Frame.MinimizedRect.Width = 688
ctprop.Frame.MinimizedRect.Height = 125
.. the size values are approx 3.125x the size entered in the object properties (on my machine anyway).