"I think it is due to the same package name in both the application."
Applications can share package names so there is a more fundamental problem here.
As Simon suggests, we need a little more information. I would have thought that debugging would have found this.
One thing that occasionally trips me up is the same ID being used for RuntimeStore or PersistentStore, so that the two applications are trying to use the same ID. I suspect something like this were something is shared that should not be is the cause. But debug to find out what.
