Ran Repair Disk on Boot Camp partition and Windows won't boot
A bit late, but maybe others still look at this.

First Aid may have messed up the partitions information. There are two separate places where the partitions are registered:


In the first sector, the MBR - this one need to identify the Windows partition plus the GUID partition range.
In the GUID table, which usually starts at sector 1, up to 63.


It is possible that First Aid reset the MBR to only list the GUID partition range (i.e. the entire disk). In that case you need to re-add the Windows partition (even if both overlap).

I've written some procedures for this here: http://blog.tempel.org/search/label/BootCamp and here: http://www.tempel.org/WindowsWithoutBootCampAssistant

You could also try to see if Boot Runner (https://twocanoes.com/products/mac/boot-runner/) helps fixing your partition and Windows boot records.