Hi, Gimmy -
This is a prime example of the risk one (i.e., your client) takes using an OS emulator instead of using the actual OS.
If this client is unable or unwilling to find/use a Windows emulator that is guaranteed to be 100% compliant or if the client is unwilling to run the (your) Windows application under a Windows operating system, then the only option I can envision would be to alter your application so that it can be optionally configured to split the currently combined and sequential actions into separate actions, where the user becomes the wait "mechanism", and has to wait for the first process to complete before manually invoking the second process.
The excellent and elegant TopWiz RunAndWait code developed by Roland Smith uses the proper, normal, standard Windows API calls for initiating the execution of a program and waiting for that program to complete. I know of no alternatives to using these WinAPI functions.
Best regards, John