I'm not sure what would cause this for IE, but some other applications have this issue. You may just need to create an Attach page/action that you run from Object Studio right before you want you spy/identify elements.
Create a page and call it 'Attach'.
Drag a Navigate stage onto the page and call it Attach.
Inside this stage, Drag the root node from the element tree onto the right side where you drop the element onto and then choose the action 'Attach' from the dropdown list on that line.
You then may need to fill in the inputs for Window Title, Process, and Child Index. The easiest way just for getting started is to put 'iexplore' for the process input and 0 for the Child Index. Then run the stage. If you only have 1 window if IE open, then it should attach to it.
Open Application Modeller and now you should be able to identify.
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Dave Morris
3Ci @ Southern Company
Atlanta, GA
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Dave Morris, 3Ci at Southern Company