The setting that I was talking about was the jonas.service.jtm.timeout. So as you said is not the problem.
As I understand the problem is related to a specific resource in your subtree.
Normally you should see error on the standard output. (not necessary on the jonas logs.)
Did you manage to make a list children as a huge tree of the thing that you tried to export ?
First of all you should check that all the previous resource could be seen on the web.
For the database corruption, I don't believe in that.
Find out the node that is sick. And tel me which one with the std output as log.