And so that people know, the new version is available. I don't know what time it was uploaded but it was before 7:00am Sydney time. To tell them apart, look at the size.
For Windows 64bit (copied from a post by PeterT)
Original: 56,762,368 calibre-64bit-0.9.16.msi
Fixed: 56,786,944 calibre-64bit-0.9.16 (3).msi
For Windows 32bit
Original: 50,897,920 calibre-0.9.16-broken.msi
Fixed: 50,902,528 calibre-0.9.16.msi
I don't have the details for other OSes but if you download now, it will be OK.