Found some more info on this.
There is a fairly understandable description of this here.
https://docs.microsoft.com/en-us/previo ... v=msdn.10)
To summarise, the hidden VirtualStore folder is part of the virtualization technology that was introduced in Windows Vista. This was intended as a compatibility feature to allow old programs to continue working when using User Account Control and running as a Standard User. It is surprising that you are encountering problems seven years later. This was a temporary fix intended to be removed in some later release of Windows.
For a program to be eligible for virtualization, it must be 32bit, not running with administrator rights and must not have been compiled with a manifest file indicating it is for Vista or later.
You can see the virtualization status of a program by adding the Virtualization column to the Processes page in Task Manager.
When a virtualized program attempts to write to a protected location such as Program Files, Windows will intercept the access denied response and redirect the write to C:\Users\<name>\AppData\Local\VirtualStore, which is a hidden folder.
When a virtualized program attempts to read from a protected location, Windows will first check for a copy of the file in VirtualStore. If it finds it, it will use that copy. Otherwise it will attempt to read from the original file.
This normally works fine if you always use the program and the files it creates from a Standard User account. You can see that if you are trying to use the files from other programs which are not virtualized or sometimes you run with Administrator rights, you will be reading and writing different locations and seeing inconsistent results. For example, you write a file to Program Files as a Standard User, it gets redirected to VirtualStore. You later run a program with Administrator rights and try to read this file. Since you are not virtualized, Windows will read directly from Program Files and not find the file there.