Windows explorer keeps handle open on executable files

I have problem overwriting any .exe from windows explorer (drag/drop or copy paste)
I receive the error message: "The action can't be completed because the folder or a file in it is open in another program". I used a sysinternal tool to check who has a hold on the said file and it is the System process.

Let say I have the following file structure
rootfolder\a.exe
rootfolder\someotherfolder\a.exe

1- If I open windows explorer into rootfolder and I drag/drop a.exe on someotherfolder, a.exe inside someotherfolder gets overwritten correctly.

2- If I have two instance of windows explorer opened at the same time, one inside rootfolder, one inside someotherfolder and I drag/drop a.exe over the other a.exe I receive the error message.

Now what's weird is if I am to close someotherfolder and try to repeat step 1, it fails with the same error message. System keeps a handle on the file for quite a few seconds until after I close the folder.

I tried turning indexing service off, I disabled UAC, I disabled anti-virus. I'm running windows 7 64bits on a domain, my user is admin of my machine, when I look the rights of the said file it says that my user has full control over it. I'm a bit clueless about what to do to solve this.