After creating an issue with the atlassian SOAP Client and updating a custom field of this issue some times, it seems that the relation between the issue and its custom field get lost.
I attached the source of the simple SOAP Client I've used.
I've executed the Client and got the output:
>Running test SOAP client...
>Successfully created issue TST-3762

So I had a look at my result at
http://jira.atlassian.com/browse/TST-3762?page=all

As you can see the update worked fine the first few times, but then the original value changed to the second updated value, and after that, the original value is empty and the custom field 'Random Text' isn't shown any more in the summary above.

To handle Jira via the SOAP interface it is very important for us, that the update of the custom fields works correctly.