Why are all paths in Clipping Masks and Compound Paths?

When I open up previous versions of Illustrator files (i.e. CS5), why are all of my paths messed up. Every object is embedded in a Clipping Mask, paths are compounded and in most cases type on a path is expanded into multiple non-editable objects. This causes complete redesign. This is terrible.

Because Illustrator accessed the PDF part of the file.
---> this points to corrupt files.
How were those files transferred to your computer? Are they on a server?
How old are they?
Which versions were they created in?
Did you already try to restart (the computer)?
Any plugins installed?

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