When progressing an issue through a workflow, specifically closing the issue;
jiraSoapService.progressWorkflowAction(soapTaken, issueKey, "2", actionParams);
I observed that any values not explictly listed in the action Params list, but shown on the Resolve screen, were cleared of their values. In particuarly, I had several custom fields that were mysteriously disappearing. It took me quite a while to figure out why simply closing a workflow item was automatically clearing out unrelated fields out from under me!
Nick Menere suggested I submit an Feature Request stating that values should retain their current values unless specifically modified.