Main reason is there are some operators (such as Gulf Air) who don't appear to understand that when something in a flight plan changes they don't cancel or change an old plan, and instead just continue submitting flight plan over the top of flight plan to the point where there are sometimes 12 flight plans for the one flight. Most systems dump the newer flight plans in the absence of a cancellation or change message, so the flight plan held by the pilot is often different to the ATC. As a result Bahrain (and the UAE for that matter) clear aircraft waypoint by waypoint until across their FIR.
Hope that answers your question. It may seem inefficient but given the number of aircraft which have unexpectedly turned towards other traffic it is a prudent safety measure unfortunately.