Autoemail will create a new call if it does not recognise the keyword in the emails subject line. Check the subject line of the inbound email and comapre it to the Subject Text field on the Update Incident tab in Autoemail. If the Subject Text field contains Update: then the inbound email will need to have Update: 1000 to update call number 1000.
If this is correct, check the database to see if you have more than one autoemailconfig table owned by different users as this could be causing this issue. You may need assistance from support if this is the case.