Hello Ken.
Those problems can be caused by a lot of things.
First, try turning on or off the "Layout Adjustment" option. It worked for me sometimes.
Second, try exporting the file as IDML and opening the said IDML. Your file might be corrupted because of a bad save (a indesign document is actualy a database).
If nothing else works, try rebuilding the document form scratch. From what i understand your documents were created with CS3 and then converted to CS6. Maby it's a conversion error.