Software Deployment

I am running into an issue to which I am unable to find the root-cause and an elegant solution.
Issue: We have received an EXE,an icon file and a config file from the development team with a specific set of req to be embedded in an mSI.
One of the req says that the EXE should run as soon as the msi is launched. Hence, to implement this have added a CA in the MSI which runs after insallfinalize.
The issue is that when the exe launches after msi install it gives an "unhandled exception" error and the eror is resolved if we copy these files in system32. Ofcourse, this solution is not a great solution and is not permissible in our environment.
The strange thing is the provided EXE works like a charm if we run it manually.

Also calling the EXE using vbscript CA doesnt work. If we copy the cscript/wscript in the same locn as in exe then the error does not appear.
It is somehow taking system32 as it's working directory and this might be the cause.
please help me understand this problem and find a solution to it.