I have been working with Illustrator since version 3. I know from experience that sometimes mysterious things happen which no that I have been able to find seems to be able to explain. I too have experienced the strange behavior of placed images changing size.
The only solution that I have been able to come up with is to delete the object and re-import it. Sometimes even that does not work. Sometimes I have to open a new file, copy everything from the old file to the new file and save the new file over the old one. Sometimes when a file does not open at all I am using Illustrator Recovery Toolbox and save them in a new file. http://www.oemailrecovery.com/illustrator_recovery.html
Obviously there is a corruption in the code, but I have not found anyone that can explain how it is happening or if there is another fix.
Fortunately, it happens VERY rarely. Perhaps, for me, less than once in...say...three hundred files, or so.
EE has a few pretty sharp Illustrator experts. Perhaps one might be able to shed some more light on this.