The StaxEventItemReader currently supports only one fragmentRootElementName. This means you cannot process files with a structure as follows:
You should be able to configure the StaxEventItemReader with a list of fragmentRootElementNames.
The workaround creating a custom MultiFragmentStaxEventItemReader extending StaxtEventItemReader as described on http://forum.springsource.org/showthread.php?88618-Reading-mutilple-element-types-with-StaxEventItemReader doesn't work. To make it properly restartable you would need access to the private XMLEventReader in the jumpToItem(int) method.