I have used subpanels within subpanels for some time and haven't had problems. Can you create a small subset of your application that demonstrates the problem? Also in general when things work in development but break with the runtime engine there is often a problem with paths and not being able to find something.
Make sure the error handling in your code can report if the sub-sub-panel vi can't be found. Most of the time LV is very good at reporting errors. However, sometimes we aren't so good at looking for them.
Finally, are you using anybody else's ActiveX controls? I have seen this sort of problem related to the Microsoft Tree Control.
Mike...
