if you were to use SharePoint Designer workflows, you'd have the same issue. SharePoint will not start declarative workflows if the intitiator is the System Account.
The only workflow that comes to mind is for you to have a Scheduled Workflow. Have it run once an hour or so, and get it to Query List your work list for item IDs where a workflow hasn't run or new items (look at creation date).
Then use a Call Web Service action to start a workflow on each item using the credentials of a System Account or some super user.