All downloads are scanned with multiple virus/malware scanners before being offered for download, and files are only accepted directly from the developer/publisher of of the software. Occasionally a malicious application does slip past the weeding process, but such are quickly removed once reported by users and confirmed by the Downloads team.
Most commonly, I see false positives arising from a particular security application using generic definitions that mistakenly flag a legitimate program as malicious. It's hard to say for sure without knowing which version you downloaded or which security application issued the alert, but I suspect that is the case here as Skype is a very well-known and respected application. Modifying lots of files is normal for most installers, so I'd expect to discover an overzealous security scanner rather than a legitimate security risk in Skype.
John
Have always trusted TechTracker with downloads, but the most recent Skype "upgrade" sent my virus checking software into a tizzy. I got so many warning messages that the install was trying to modify various files that I aborted the install. I would have thought that these downloads would be thoroughly tested before adding them to the downloads.

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