Software Deployment

Hello,
This post in concern to problem with Short Cut of an application.
Back Ground-

Case 1. [2008]

We have one application that was installed in 2008 through .exe [I am not very much sure but it was deployed through SMS on 700-800 machines]. This .exe deploys a RDP file in C > Program Files > Test Folder. also it creates a shortcut in Start > All Programs > Applications > Test Application [ABC] [when we right click on ABC application then it points out to RDP file ]

Case 2. [Sept]
Now I modified that RDP file while amending some x , y numbers so that once it executes should not come with full screen because everytime user needs to minimize this remote screen to get back to their mails and other desktop things. Now It was deployed through SMS near around on 300 machines and it was deployed successfully. MSI replaced the old RDP file with updated one. And shortcut as usual was pointing out to that RDP file and continuted to point out the same.
Case 3:

There was some problem with resized window because for desktop users it worked well but for laptop users is was squezeed.
So technical lead created a VB script. When it is double clicked, it creates a RDP file automatically in C > Users > Temp folder. [every time when VB file is hit, this RDP files gets created]
ISSUE-

This MSI was deployed on two machines.
One who have the case 1 means old version 2008 and at other side on Case 2 i.e. SEPT version. This was done because of maintaining consistency at both sides of users.

In .MSI - I added VB script file in FILE module of WISE and created short cut that points out to this vb script in "C > Program Files > Test Folder > XYZ.vbs". Also in FEATURES module, I created USER and then Machine [Machine as a child, User as Parent and creating shortcut in respect of Machine]

No Command line, No upgrades have been defined.

But when this MSI was deployed via XML through SMS then it nicely puts that vb script in "C > Program Files > Test Folder" [Now two files exist in Test folder, RDP + VB script]

But when I click on start > Applications > ABC aplication, right click on it, it still shows target to RDP file and not VB script.
This was tested on 4-5 virtual machines [phyical prescence] and everything went well. But really surprised whats happening now.

REMOVAL of Older Version-

If anyhow we arrnage old version as well [in 200-200 slots of users] and replace with new VB file but older version is not in Add Remove Programs as well and that was deployed through .EXE [2008 version].

Please give your suggestions on this asap.

Thanks and Regards,