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I have been searching for the answer, but couldn't find any that would explain it completely. It is more complicate to google because somehow it ignores those $$ marks even when entered with quotes.

The only thing clear is that $$PendingFiles directory is part of installation or update process and it most likely appears if one has moved the Program Files or ProgramData directory to another drive and linked it with junction.

Update: The resources I found are: http://www.runsmall.com/2011/08/index.html and http://www.sevenforums.com/crashes-debugging/168933-error-has-occurred-not-all-features-were-successfully-changed.html, but none of them explains why the directory is created and what exactly creates it.

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"The only thing clear is that ..." - That's the info. I found as well: 1, 2. – Karan Jan 2 at 4:09
@Karan Yes, those are the same resources I referred to. I guess I'll have to add them to my question to make it clear. – AndyDeGroo Jan 2 at 5:03

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Windows can't update hardlinks when they are in use, so the updates are installed during shutdown/boot. The new files are stored in this PendingFiles directory. Nobody outside of MSFT can answer how in detail it works.

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