Weird… On x86_64 Linux everything is OK.
$ rustup update
info: syncing channel updates for 'stable-x86_64-unknown-linux-gnu'
info: syncing channel updates for 'nightly-x86_64-unknown-linux-gnu'
info: checking for self-updates
stable-x86_64-unknown-linux-gnu unchanged - rustc 1.14.0 (e8a012324 2016-12-16)
nightly-x86_64-unknown-linux-gnu unchanged - rustc 1.16.0-nightly (2782e8f8f 2017-01-12)
And my x86_64-pc-windows-msvc nightly installation also updated without problem, so maybe update again?