Have you checked the amount of data that is being returned from the SOAP call?
I have had cases where the amount of data being returned was over the upper limit for the CAPA Web Services and was just truncated by the CAPA SOAP call.
I believe the default OOTB maximum result length was 1,048,576 bytes, (after opening a case for this issue) I ended up increasing my limit to the maximum suggested value of 4,194,304 bytes.
In the few cases where even that isn't enough, I am using a PowerShell script to call the WebService and parse the results to something more manageable for me (or parsing them right to an SQL table).
The maximum result length can be found on the Configuration tab under Modules / Web Services - SOAP Module
Hope this helps!
Ian