I just encountered the same problem. I solved it on my own.
If you are using a windows-based Eclipse, you may follow these steps below:
Open "Run As" --> "Run Configuration" on the project you want to export
Click "Search" for Eclipse to refresh the list of main class
Then export the Runnable JAR file again, and everything goes smoothly.
Please let me after completing those steps if it is not working. We may find another way.