Link source changed after packaging

Hi!
I have a book with several files. Each file has several links ( to images). Images are located on the file server, few of them are on my own computer. After making a package for printing, all the link sources in the original file changed. Now all the links point to "Links" folder that is in that package folder. Is that normal? Or it's some kind of bug? I'm confused why did that happen.. except one .ai file that I used for logo in each file didn't change it's source... Now I have to relink each image...
I'm using latest InDesign CC, Windows 7.

continuing... But I have CS6 8.0.2 perpetual - not CS6 from the Creative Cloud (CC), so it is I think a few versions behind the one you download or update from the cloud. I just tested it again and it is fine.
BUT InDesign CC2014.1 does mess-up the original files and saves them if you choose "Update Graphic Links in Package", it links them BOTH to the package, no good.
I don't have the latest CC2014.2, not sure how that behaves.
If you DON'T check "Update Graphic Links in Package" then it doe not re-link or save the original (unless yo didn't save before packaging then of course it does save but not relink original. But then the Packaged files are not re-linked either.
Bummer.  So making a copy of the original files is the easiest workaround (or a 3rd-party packager plugin or app would work too, I hope--don't have one of those anymore)

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