When an item is updated maually the event reciever starts and work as expected. But when the item is updated through a SharePoint Designer Workflow, nothing happens. There is nothing about this in the logs.
Actualy according to sharepoint workflow architecture updates is not commited to database right after activity axecutes. The actual commitment will be done by WorkBatch service right before the workflow is persisted. Are you shure that event reciever is not fired at all? And is there any System.Workflow-related event in ULS logs?
If a list has workflows defined which are set to auto-start, these will always execute before any other 'ItemUpdated' or 'ItemCreated' event receivers by default. It is possible to re-order these in code.