Software Deployment

Hi All!
I am new to MSI Development. I am working on an MSI which works fine when it was executed using MSIEXEC command on a virtual machine. Now when I gave this MSI to the department who are responsible to distribute it via GPO and asked them to ditribute this MSI to a test machine using GPO, they did that but the MSI is not working in the same way as it did on the virtual machine. For example, when the MSI was executed using MSIEXEC on the virtual machine, it created a folder called ApplData (when the folder is already present, the installation over writes it) under C Drive and also it created some registry entries with the required permissions to the user. And when I go to Add/Remove programs on this virtual machine and remove the program I have installed through MSI, then the folder that was created under C Drive was removed and the same happened with the registry values it created. But on the test machine, when the same MSI was distributed through GPO, it is not over writing the folder under C Drive and also the appropriate permissions are not getting granted to the registry entries and because of this the operation of the program is getting failed.

Can any one please let me know what I have to do in this issue?
I would appreciate their help, very much.

Regards,
Satish