I missed Vista entirely (thankfully) and had Windows 7 installed on my office PC earlier this year. I spent all day yesterday trying to get changes in an apache conf file to have some effect.
I was in apache's bin directory typing the following command:
htpasswd.exe -cb "C:\Program Files\Apache Software Foundation\Apache2.2\htpasswd\passwords" username password
Of course the file never appeared where I asked for it to go, but there was no error.
So after searching the c drive I found it - you know where - C:\Users\user\AppData\Local\VirtualStore\Program Files\Apache Software Foundation\Apache2.2\passwd.
SO I asked a program to create a file somewhere and the OS decided to put it somewhere else?
Really - what's MS up to? Is their OS security is so bad, that they have to come up with this sort of bullshit? I just don't get it.
As another poster pointed out if you don't install your software in the Program Files folder (like python) none of this happens.
What a waste of time.