Hi Jacob,
When this issue is started? Is this started recently upon changing any customization/enhancements in SAP EM.
1. Is this happening for one event type or for all event types against event handler type?
2. Application system uses event type together with tracking id to assign to event handlers. When the data send it from SAP EM, it refers same event handler for multiple tracking id's and posting his control parameters as well.
3. Go to Event Handlers -> Define Activities for Updating Event Handlers and check any custom function and update which you send data causing the issue.
Clean up: I don't think we have a custom tool to clean up control parameters and tracking ids. However you can go to each and every handler delete but it is tedious job to perform.
Regards
GGOPII