I'd achieve this by downloading Flex 2. With this tool you can view all of the variables, functions and procedures that are in an app.
Go to the patches tab, press the '+' symbol and locate the app to create a patch for. Then process the app by tapping it - don't worry about adding patch name.
Next, when you're inside the processed app you need to press "Add units". This will allow you to add overrides so that you can change what functions return and such.
Anyway, from here, you need to select a class to look inside. The jailbreak detection functions and variables are always stored in the executable. Tap the app name again at the top of all the classes under the 'executable' tab. Then just search.
Just search for "jailbreak" or "jailbroken" and if the app is running checks then it will return functions and vars related to this. I am yet to see an app that runs this check with a different function name that does not include "jailbreak" or "jailbroken".
If you'd like, I can show you how to override this detection.
I suggest you try the app "highway rider", because that has detection and you can easily see, and override it nice and easy and get the startup warning to go away if you want!