Is it possible that the shim does not have enough rights on the file? From the trace, it seems unable to move the file using java native methods and thus tries a copy/delete sequence. On Linux, failure to move the file is either because of:
* missing file rights
* source and target are on different mount points.
In both cases, the shim falls back to a copy/delete sequence. If it fails to delete the original file after the copy, then you can see this scenario.