Detecting External Apps?

I am writing a usability testing application, it starts the screen recording, gives the user tasks, and then when finished brings up a survey and stops the screen recording. My problem lies in the last part of this process, because the screen recording app brings up a msgbox when recording is over saying where the file is put and then when that is closed it brings up the screen recording application. I am trying to block the user from seeing this so am currently using the following method.

Private Sub WatcherHandler(ByVal sender As Object, _
ByVal e As System.IO.FileSystemEventArgs) Handles FileSystemWatcher1.Created
Dim Camtasia As Integer

[code].....

Basically when the msgbox from the screen recorder comes up it means a file has been created...so the folder is watched and when the file is created the msgbox is checked for, when it exists a short timer is enabled and then knowing the window exists it is hidden using showwindow findwindow approach. Although this approach does work, Camtasia needs to be closed and re-opened after in order to record again and for some reason it does not always work.