Failing script producing extra folder

I've run into an error that I'm not able to understand and fix despite extensive web searches over the past few days.

I have a SetupComplete.cmd script under this location D:\RemoteInstall\Images\WIN 7\install\$OEM$\$$\Setup\Scripts. This script maps a network drive and then runs another script to install a bunch of apps silently. This was working fine until few days back; it started giving out an error:

Windows cannot find the blah blah (apps). 
Make sure your name is typed correctly and so on. 

I tried everything from running anti-virus, malware, checking environment variables, cmd.exe inside system32 folder, you name it, none of it worked. I then re-install Server 2012, tried all over again, same result. The script runs at the FirstLogon in unattended install but fails with the same error.

I ran the SetupComplete.cmd both as an Adminstrator and as a user to see if it runs and does what it's suppose to do. It ran, but it threw up a different error directly from the server, saying:

Windows cannot access \10.8.8.3\Apps\Apps\7-Zip\x86\7z1506.exe.  
Check the spelling of the name, there might be problem with your network.
Error Code: 0x80070002  The System Cannot find the file specified.

What I found weird in the script is that it adds one extra Apps folder name into \10.8.8.3\Apps\Apps when it should be just one Apps folder, as it was before a few days ago. When I open up the SetupComplete.cmd, it only shows one Apps folder, but when I run it, it shows two Apps folders. This is where the problem is because an extra Apps folder is preventing the apps from installing silently.

I'm not able to understand how this extra Apps folder is showing up when running the script. I even deleted and re-created a new SetupComplete.cmd script, and also the file Script.bat, which contains all the switches to install the apps silently. It didn't work.