Permissions issues after installing Windows 10

[Brent Epp]

I recently (finally) installed Windows 10 on my system (clean install).  
All of my files are stored in on a secondary drive/partition, on which 
cygwin is also installed.  I expected to be able to just pick up where I 
left off, but I'm getting all sorts of permissions issues with cygwin.  
I did run the cygwin setup again to reinstall/upgrade.

First, I had restore my cygwin home directory from a backup, since it 
was giving me permissions errors on .bash_history, .ssh, etc, but the 
biggest headache is with git repos.  First, it gives a "fatal: unsafe 
repository" error.  If I add it to the safe directories list, it git 
still has to reindex the repo every time I run `git status`, and it 
still fails when I try to enter a commit.

It seems most or everything is owned by "Administrators".  The only way 
I've been able to fix this is to go through the Windows advanced 
permissions dialog, change the owner to my user, and set all sub-objects 
to inheritable permissions, but I'm very leery about mass changes like 
this.

Why did this happen?  And is there a better/safer/correct way to fix this?

Thanks
  - Brent