This is all I could find on it, not sure if it will help you at all. As far as I can tell your only option is to do what you have done. Wipe the phone and reload the OS. I would try again and see if you get a different result.
Error 543 (VM_FS_MISMATCH): Incompatible Java filesystem installed
The VM has detected that the OS binary is different than the OS binary used to create the Java file system. This means that the Java native methods may not be linked properly and as such, the integrity of the system cannot be guaranteed. The system can be recovered by using the VM DLFX and DLPS commands to delete the fixups and persistent store. This will clear all data and fixups and let the filesystem relink to match the new OS binary. The recovery order is important: 1) Delete Fixups 2) Delete Persistent Store 3) Reset device. http://www.blackberry.com/knowledgec...00443&vernum=3