Well, this is a tough one! I've gotten this error before with a different file. In my case, the error occured when the Application Builder was supplied with two paths to the same external library, as opposed to a VI in your case. I had inadvertantly included a DLL as a support file in the Application Builder, but it was also loaded by one of the VIs in their application. For instance, if you build a Data Acquisition VI and you also include lvdaq.dll as a support file, you have actually provided the path to this DLL twice, once through the support files and once through the DAQ VIs. To resolve this, I removed the DLL or from the support files and it worked. Your case may be similar. See if there are multiple places you're including any external library or other dependency file.
Also, if you're using LabVIEW 6.0, here's a possibility.
This Knowledgebase was written for TestStand but mentions a bug in the App Builder for LabVIEW 6.0 that caused an error message much like the one you're receiving. Let me know if any of this helps or if you're still getting the error.