InstallShield installation has different Current-Directory to Deployment installer

Question

my C# application built using Visual Studio 2010 had a deployment project which was being used to build an .MSI installer. Since we know we'll need to upgrade VS pretty soon and we know that later editions won't support the .vdproj, I've started to rebuild the installer using InstallShield.

Both the old and the new installers install the application in Program Files, but when I run the resulting executables the version created using InstallShield seems to start with a different current directory setting.

If I run the installed executable using our old installer (vdproj) and get it to output the current directory it returns:

C:\Program Files\MY_APPLICATION

...which makes sense since this is the folder in which the application is installed. But if I run the installed executable created by the InstallShield installer, the result of Directory.GetCurrentDirectory() is always:

C:\Documents and Settings\USERNAME

Now, I know I can just set the current directory on start-up, but I was wondering whether there was just some kind of setting in InstallShield I could use instead.

Many thanks in advance.