TC is closing an appliaction and it should not be

At certain points in our program’s execution, we will launch a secondary application and it will display a browser control. This secondary app might be used multiple times in a row, or might close and be reopened later on.. whenever we have closed it, the next time it launches, we get errors in our test logs. This is not an error condition, it is how our software works. We would like to know how we could tell TC to expect a window to be launched at a certain point in a new process (or re-launched by an existing process).